SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
htseq-count low count problem gandalf886 Bioinformatics 3 08-23-2014 07:05 AM
inconsistency between samtools mpileup and igvtools ynwh Bioinformatics 4 09-06-2013 11:11 AM
igvtools window functions mbk0asis Bioinformatics 0 06-13-2013 08:54 PM
HTseq count problem dietmar13 Bioinformatics 0 12-19-2012 02:34 AM
IGVtools 1.5 not showing bam alignments ketan_bnf Bioinformatics 8 03-08-2011 11:20 PM

Reply
 
Thread Tools
Old 02-09-2017, 06:33 AM   #1
tristan dubos
Member
 
Location: France

Join Date: Dec 2015
Posts: 39
Default Problem igvtools count

Hi ,

I would like to detect some genome position indel. So i decide to use igvtools count to extract details for all position sequenced in my 900 dataset. I used for every amplicon this command :

Code:
bash igvtools count --query=chr1:162741785-162741920 --strands read -w 1 --bases data_sorted.bam positions_amplicon.wig hg19.fa
I got this kind of result ( output file positions_amplicon.wig) :
track type=wiggle_0
#Columns: Pos, Positive Strand A, Positive Strand C, Positive Strand G, Positive Strand T, Positive Strand N, Positive Strand DEL, Positive Strand INS, Negative Strand A, Negative Strand C, Negative Strand G, Negative Strand T, Negative Strand N, Negative Strand DEL, Negative Strand INS
variableStep chrom=chr1 span=1
162741785 2638.0 0.0 1.0 0.0 0.0 0.0 0.0 2535.0 0.0 3.0 0.0 0.0 0.0 0.0
162741786 0.0 2640.0 0.0 0.0 0.0 0.0 7.0 0.0 2540.0 0.0 0.0 0.0 0.0 0.0

Problem : for my 92 amplicon i test in 900 dataset (add by genomic position ) i found the last columns always equal to 0 , that mean Negative Strand INS never appends in my reads alignments. I check some data with igv graphic and there is Negative Strand INS in some position.

Is my command wrong ? or is there some bug in igvtools ?

Best regards ,

Tristan
tristan dubos is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 03:59 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO