Converting Bam file to Fasta (Zipped)

Converting Bam file to Fasta (Zipped)

0

I would like to convert .bam files to fq.gz (zipped fasta files) for paired reads.

bedtools bamtofastq seems to be a commonly recommended method, I have also seen samtools fastq as a possible alternative.

bedtools bamtofastq -i inputfile.bam -fq outputR1.fq -fq2 outputR2.fq 


samtools fastq -@ 8 unmapped_sorted.bam \
  -1 outputR1.fastq.gz \
  -2 outputR2.fastq.gz \
   -0 /dev/null -s /dev/null -n

It seems for bedtools bamtofastq it is not possible to output zipped fasta files.

Is samtools fastq a good alternative?


samtools


bamtofastq


bedtools


paired

• 37 views

updated 1 hour ago by

5.1k

written 3 hours ago by

0

Read more here: Source link