tag:blogger.com,1999:blog-6721211197199573684.post3470210019894868165..comments2024-02-23T00:25:42.548-08:00Comments on Recipes, scripts and genomics: How to read BSMAP methylation ratio files into R via methylKitUnknownnoreply@blogger.comBlogger29125tag:blogger.com,1999:blog-6721211197199573684.post-53313189221094811682022-12-28T02:59:05.513-08:002022-12-28T02:59:05.513-08:00One of the most crucial pieces of knowledge for me...One of the most crucial pieces of knowledge for me is this. We occasionally compete with one another. When we play online games, we believe that the number of spacebars we use is crucial. You can increase your spacebar count here. For further details, go here <a href="https://we.riseup.net/spacebarcounter/spacebar-counter-test-your-clicking-speed" rel="nofollow">spacebar click counter</a>.marryhttps://www.blogger.com/profile/10888362487714215662noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-76432702956733718022022-12-09T00:41:31.426-08:002022-12-09T00:41:31.426-08:00You are to be thanked for sharing this significant...You are to be thanked for sharing this significant piece and for this truly outstanding profile. I'm going to share a phony Twitter account-generating profile with you. With the aid of a fake Twitter account generator, you can create a celebrity account without registering and share it with your close friends. For additional information, see this profile <a href="https://app.roll20.net/users/11375907/fake-twitter-profile-generator" rel="nofollow">create fake twitter account</a>.Sharon Johnsonhttps://www.blogger.com/profile/15113783573537223819noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-16081022569713252812022-06-18T03:28:03.839-07:002022-06-18T03:28:03.839-07:00A fine quality educational blog! I like the way bl...A fine quality educational blog! I like the way blogger presented information regarding the concerned subject.<br /><a href="https://getpocket.com/my-list?src=sidebar" rel="nofollow">Best engineering college in Dehradun</a>ADMINhttps://www.blogger.com/profile/15857678683276899904noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-34354868464903933302021-05-26T02:54:18.128-07:002021-05-26T02:54:18.128-07:00read()からmethRead() read()からmethRead() M.Kenthttps://www.blogger.com/profile/04255885436810669845noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-78501297374631699892021-05-25T07:32:24.170-07:002021-05-25T07:32:24.170-07:00Original BSMAP is so old that a little bit difficu...Original BSMAP is so old that a little bit difficult to install(because of difference of char), and improved one is posted on github as BSMAPz.<br />https://github.com/zyndagj/BSMAPz<br /><br />Methylation ratio file generated from BSMAPz's methratio.py has a difference in context section. It's already written as CHH, CpG, CHG(not like CGCGT).<br /><br />Then maybe this awk will be working if you use BSMAPz and added the command "-i no-action"<br /><br />awk '($4=="CG")' BSMAPzexample.txt > CpG.txtM.Kenthttps://www.blogger.com/profile/04255885436810669845noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-14544786005688887372021-03-25T06:29:33.844-07:002021-03-25T06:29:33.844-07:00I have a bed file output from bsmap consisting of ...I have a bed file output from bsmap consisting of chr, start, end, methylation ratio, coverage but the strand is split by coverage (eg. 36 sites split into 31 on + strand and 5 on – strand). So how can I prepare the strand column for methylkit read function? saimahttps://www.blogger.com/profile/02510515632555703798noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-76604911974587200682019-05-15T16:09:41.895-07:002019-05-15T16:09:41.895-07:00If I have 14 BSMAP methylation ratio files how to...If I have 14 BSMAP methylation ratio files how to I read all of them in as a list, like you are supposed to in the methylKit process?Anonymoushttps://www.blogger.com/profile/02866909663785916453noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-13571123689264154382017-06-08T10:19:18.862-07:002017-06-08T10:19:18.862-07:00I should note that a column was added for start an...I should note that a column was added for start and stop information ($2 and $2-1) this is in case you want to visualize the data downstream as BED format file require start and stop information.Anonymoushttps://www.blogger.com/profile/15034059216816910574noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-9434477240362398292017-06-06T13:09:11.224-07:002017-06-06T13:09:11.224-07:00For those interested in what and awk statement wou...For those interested in what and awk statement would look like for all C contexts:<br /><br />awk '(NR>1){if(($3=="-" && $4~/^.CG../ ) || ($3=="+" && $4~/^..CG./)) print $1"\t"$2-1"\t"$2"\t"$3"\t""CG""\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12; else if(($3=="-" && $4~/^C[AGT]G../ ) || ($3=="+" && $4~/^..C[ACT]G/)) print $1"\t"$2-1"\t"$2"\t"$3"\t""CHG""\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12; else if(($3=="-" && $4~/^[AGT][AGT]G../ ) || ($3=="+" && $4~/^..C[ACT][ACT]/)) print $1"\t"$2-1"\t"$2"\t"$3"\t""CHH""\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12; else print $1"\t"$2-1"\t"$2"\t"$3"\t""CNN""\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12}' BSMAPratio/infile.txt > BSMAPratio/BSMAP_outfile.txt<br />Anonymoushttps://www.blogger.com/profile/15034059216816910574noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-72264030372209486332017-06-05T14:07:27.347-07:002017-06-05T14:07:27.347-07:00Because the position will change depending upon th...Because the position will change depending upon the strand which the cytosine is present.<br /><br />Example:<br />strand context type<br /> + CTCGT CGH<br /> - TCGTT CGH<br /> - GTGCT CHH<br /> - CGGTT CHG<br /><br />The context is printed in relation to only the + strand. <br />This regular expression will only find cytosines in the CG context. When the cytosine is on the + strand it is in the 3rd position. When the cytosine is on the - strand there should also be a another cytosine in the 2nd position (complementary to the G on the - strand).<br /><br />It matters that you not just specify 'CG' as a CG can be in a different location for some lines (see the 4th line in my example, a CG is present but it is a CHG context).<br /><br />Anonymoushttps://www.blogger.com/profile/15034059216816910574noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-90958059633089453032016-08-31T18:23:10.198-07:002016-08-31T18:23:10.198-07:00Why is the position of the CG important? And why ...Why is the position of the CG important? And why is the position of the CG different on the - vs + strand? (^.{2}CG vs ^.{1}CG). <br /><br />I'm trying to calculate Cs in CpG, CHH and CHG context and it would be nice to know what is going on.Unknownhttps://www.blogger.com/profile/13849824585265366437noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-35277757742072850602015-11-25T21:28:29.113-08:002015-11-25T21:28:29.113-08:00This comment has been removed by the author.vnahttps://www.blogger.com/profile/00111386368730986200noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-32047695569460758962014-06-16T19:54:24.711-07:002014-06-16T19:54:24.711-07:00This comment has been removed by the author.varsharaohttps://www.blogger.com/profile/06311661304565504019noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-4401781310787237272014-05-27T06:33:38.040-07:002014-05-27T06:33:38.040-07:00Great post! Thank you so much for sharing..
For ...Great post! Thank you so much for sharing.. <br /><br />For those who want to learn R Programming, here is a great new course on youtube for beginners and Data Science aspirants. The content is great and the videos are short and crisp. New ones are getting added, so I suggest to subscribe. <br /><br /><br /><a title="R Programming For Beginners" href="R%20Programming%20For%20Beginners" rel="nofollow">https://www.youtube.com/watch?v=BGWVASxyow8&list=PLFAYD0dt5xCzTQHDhMPZwBoaAXWeVhZzg&index=19</a>Selva Prabhakaranhttps://www.blogger.com/profile/05519694374996247829noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-38979181312280705832013-08-09T00:15:46.296-07:002013-08-09T00:15:46.296-07:00Thanks for the update Claire!! Thanks for the update Claire!! altunahttps://www.blogger.com/profile/04295081899402275119noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-67203637787549556072013-08-05T07:24:48.922-07:002013-08-05T07:24:48.922-07:00Hi,
So i contacted the authors. They said that th...Hi,<br /><br />So i contacted the authors. They said that the eff_CT_count is new and is calculated by adjusting the methylation ratio for the C/T SNP, using the reverse strand mapping information. It's also possible to turn off these columns when you use methylratio.py by using this parameter '-i no-action'.<br /><br />Therefore, the 'C_count' and 'CT_count' columns correspond to the 'total_C' and 'methy_C' column headers respectfully.Claire Morganhttps://www.blogger.com/profile/18290108342818087106noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-84264531324038051102013-07-29T07:10:02.508-07:002013-07-29T07:10:02.508-07:00I've contacted the BSMAP team and will respond...I've contacted the BSMAP team and will respond as soon as i get an answer.Claire Morganhttps://www.blogger.com/profile/18290108342818087106noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-23376088336850245092013-07-29T07:09:18.382-07:002013-07-29T07:09:18.382-07:00This comment has been removed by the author.Claire Morganhttps://www.blogger.com/profile/18290108342818087106noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-77513887768367128982013-07-24T11:47:06.313-07:002013-07-24T11:47:06.313-07:00Hi,
I don't have the most recent version of th...Hi,<br />I don't have the most recent version of the BSMAP but I think they usually describe the output in a readme file or in the script help. I think eff_CT_count or CT_count is now replaced the total_C. The best I can suggest is to find the readme or help page where the output is described and/or take it to the authors of BSMAP. and I would appreciate it if you can post the answer as a comment here.<br /><br />Bestaltunahttps://www.blogger.com/profile/04295081899402275119noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-81655789926663263502013-07-24T11:26:37.738-07:002013-07-24T11:26:37.738-07:00Hello,
Firstly, thanks for posting details on how...Hello,<br /><br />Firstly, thanks for posting details on how to use methylKit on BSMAP.<br /><br />I have recently installed BSMAPv2.74 and the methratio.py program outputted a file with the following headers:<br /><br />chr <br />pos <br />strand <br />context ratio <br />eff_CT_count <br />C_count <br />CT_count <br />rev_G_count <br />rev_GA_count <br />CI_lower <br />CI_upper<br /><br />I can't find documentation that will help me relate these 11 headers to the 9 headers you have written about in your initial post. Some of them are of course obvious, but I'm quite confused trying to link 'total_C' and 'methy_C' with 'eff_CT_count', 'C_count' and 'CT_count'.<br /><br />Do you know the answer, or could you post a link to where this might be described?<br /><br />Kind regards<br />Claire Morganhttps://www.blogger.com/profile/18290108342818087106noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-67557162072924836362012-12-29T09:17:01.816-08:002012-12-29T09:17:01.816-08:00Wonderful! Thank youWonderful! Thank youAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-2647908543568450382012-12-28T15:32:20.806-08:002012-12-28T15:32:20.806-08:00you should be able to give a list of file location...you should be able to give a list of file locations, keep the "pipeline" argument as shown above, give "sample.id" as a list, also use "treatment" argument, And that will read a list of files and produce a methylRawList<br /><br />some thing like the following (file.list is a list of file locations)<br />myobj=read( file.list,pipeline=list(fraction=TRUE,chr.col=1,start.col=2,end.col=2,<br /> coverage.col=6,strand.col=3,freqC.col=5 ),<br /> sample.id=list("test1","test2","ctrl1","ctrl2"),assembly="hg18",treatment=c(1,1,0,0))<br /><br />altunahttps://www.blogger.com/profile/04295081899402275119noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-12547980521249754992012-12-28T14:14:30.264-08:002012-12-28T14:14:30.264-08:00Hi, Thanks for the info on reading in the BSMAP f...Hi, Thanks for the info on reading in the BSMAP files. It was really helpful. I<br /><br /> was wondering if you have any advice for generating a methylRawList from individual files that were read in this way. <br /><br />The example given in the read{methylKit} help file only shows how to generate a methylRaw object from 'generic' files, I can't figure out how to rework the example to generate a methylRawList from these individual objects.<br /><br />ThanksAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-89889930871518447312012-12-11T08:50:29.788-08:002012-12-11T08:50:29.788-08:00I think not, BSMAP readme.txt documents says that ...I think not, BSMAP readme.txt documents says that the strand of the 5bp sequence is the plus strand irrespective of the strand of the covered CpG . So a CpG on the minus strand will appear as ".{1}CG". For example, If the strand="-" the following string denotes a CpG on the minus strand: ACGAA. The minus strand of the same string will appear as: TTCGT altunahttps://www.blogger.com/profile/04295081899402275119noreply@blogger.comtag:blogger.com,1999:blog-6721211197199573684.post-62225127054736249642012-12-11T02:03:01.160-08:002012-12-11T02:03:01.160-08:00I think it should be awk '($3=="-" &...I think it should be awk '($3=="-" && $4~/^.{2}GC/ ) || ($3=="+" && $4~/^.{2}CG/)' BSMAPexample.txt > CpG.txt ( for minus strand it should be ($3=="-" && $4~/^.{2}GC/ ))Anonymoushttps://www.blogger.com/profile/13020768965038371612noreply@blogger.com