Modifying bam file sequence names according to 2nd column
Hi,
I want to modify the sequence names in my bam file. They're supposed to be for paired end, but the names don't have /1 and /2 so I can't use software like bedtools bam2fastq. Anyway, I'd like to add /1 to the end of the name if the flag in the second column is 99 or 83 and then /2 if its 163 or 147. For instance,
HSQ1008:141:D0CC8ACXX:3:2202:1520:59984 163 chr14 105899906 60 101M = 105900110 305 CCTTTCCAGGAAAGGGAGTAGCGAGGCTGCTCACTTAGAGCCACGCACCTGGGGCTGACAGTGTGCCTGGCAGTACCTGTGTGGAAAGACAGTTACAGAGG @C@DDFDDHHHHAHGBHG1AFHIGIJGIIGEIJIGIFE?BBGIIIIBHIEGHHHFFFEEEEEEDCCCCCDDCD?CACCDDDCBB@ACBC?CCDCCCACAC8 RG:Z:NA12877 XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:101
should become
HSQ1008:141:D0CC8ACXX:3:2202:1520:59984/2 163 chr14 105899906 60 101M = 105900110 305 CCTTTCCAGGAAAGGGAGTAGCGAGGCTGCTCACTTAGAGCCACGCACCTGGGGCTGACAGTGTGCCTGGCAGTACCTGTGTGGAAAGACAGTTACAGAGG @C@DDFDDHHHHAHGBHG1AFHIGIJGIIGEIJIGIFE?BBGIIIIBHIEGHHHFFFEEEEEEDCCCCCDDCD?CACCDDDCBB@ACBC?CCDCCCACAC8 RG:Z:NA12877 XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:101
How should I go about this? The bam file is also missing header information. Thanks!
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Filling gaps in BAM file
written by hemr3 •
-
extract discordant,split reads from BAM file
written by 9521ljh •
-
Trimmed NGS exome data failed to be mapped with bwa
written by yanqiangchang •
-
Can't convert paired end BAM to bed using bedtools
written by colin.kern
-
BWA: improper orientation but listed as properly paired
written by richard.deborja
-
[Samtools] How to extract reads matching a given sequence
written by madkitty
-
Question About Bwa Pe Mapping And Calling "Properly Mapping Pairs" In Samtools
written by neal.platt
-
Should We Dump Illumina Pair-End Mapping Results In Sam With Mapq=0, But Good Template Length
written by PeterPan •
-
How To Extract Reads With Wrong Insert Size With Samtools
written by Assa Yeroslaviz
-
Bam File Output Format .. Don'T Understand!
written by madkitty
I think you should be able to use Picard Sam2Fastq on this bam file and still able to get a pair of fastq files as output. You don't need to add
/1or/2in the bam file. The/1and/2tags are trimmed off from the paired-end reads before they are written in the bam file. However, this information can be deduced using the samtools bitwise flag (second column). As you mentioned that 99 and 83 will represent/1reads. Sam2Fastq also uses the same logic to assign the_1and_2tags to the reads. You will have to make sure that you create a proper header for the bam file in case it is missing one. Read about the SAM format here https://samtools.github.io/hts-specs/SAMv1.pdfyou already asked a very similar question: Substitute first column based on second column
why would you need to to this ? what's your final aim ?
I'm just trying to convert a bam to a fastq file, but the paired reads have duplicate names rather than /1 and /2. I tried using Hydra bamtofastq and this seems to work, so my question is resolved. Thanks!
Hello jyu429!
It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=58344
This is typically not recommended as it runs the risk of annoying people in both communities.
Ah, sorry. I wasn't sure how to delete it, but it won't happen again.