Question: duplicate read names in TCGA raw bam file
1
gravatar for jonessara770
23 months ago by
jonessara770130
jonessara770130 wrote:

Hi,

I downloaded some TCGA ExomeSeq bam file and would like to convert them to fatsq. Picard can not convert them because there are some reads with identical same readname in the bam files. As suggested by the community bedtools bamtofastq can randomly choose only one of these reads and put it to fastq file. I tried bedtools bamtofastq but the duplicate read names are still in the fastq output.

My question is :

  • Why there are reads with identical readname in bam files?
  • How can I fix this issue? should I rename the reads name in fastq files?

Thanks Sara

dnaseq • 1.1k views
ADD COMMENTlink written 23 months ago by jonessara770130

Possible that the R1/R2 identifiers were stripped from the reads? Multi-mappers?

ADD REPLYlink modified 23 months ago • written 23 months ago by genomax66k

No there are there. this is output of bedtools bamtofastq

fastq1

@C0UL8ACXX120727:8:2301:17486:13986/1

@C0UL8ACXX120727:8:2301:17486:13986/1

fastq2

@C0UL8ACXX120727:8:2301:17486:13986/2

@C0UL8ACXX120727:8:2301:17486:13986/2

ADD REPLYlink modified 23 months ago • written 23 months ago by jonessara770130

An identical issue was discussed in a recent thread. Edit: Unfortunately there was no clear solution (check out the thread yourself: Remove duplicates reads Ids ).

ADD REPLYlink modified 23 months ago • written 23 months ago by genomax66k

I've had the opposite problem (bedtools bamtofastq did not give the required results, Picard tools did the job), but with single end data, so I don't know what would happen for paired-end reads.

The bam files had multiple entries for some of the reads, which were multi-mappers. With bedtools bamtofastq the multi-mapping reads ended up present multiple times in the fastq file. Picard tools ran without any errors and gave only 1 copy of each read in the fastq file.

ADD REPLYlink written 23 months ago by mastal5112.0k
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