error: BAM to FASTQ
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Entering edit mode
23 months ago
mailard • 0

Hi! I run

samtools bam2fq bx_mapped.bam

and my result is

[E::sam_parse1] no SQ lines present in the header [bam2fq_mainloop] Failed to read bam record.
[bam2fq_mainloop] Error writing to FASTx files.: No such file or directory [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 0 reads

How can I fix it?

Thank you for your answer!

convert bam fastq samtools • 929 views
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Entering edit mode

Try remapping your BAM (which aligner did you use?). It looks to be corrupted/incorrect as the header does not contain reference chromosome lines.

samtools view -h BAMFILE | less
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I use histat2 Thanks for your help, I decided my problem!

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