unalign bam and convert to fastq
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As said, convert the bam to fastq and re-align with whatever tool you are interested in. Keep in mind about Paired-End, soft/hard clipping etc while converting to fastq.
Or tell what is meant by unaligned bam? Do you mean to say extract unaligned reads from bam?
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Ram
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GouthamAtla
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GouthamAtla
Basically our data has indels in it that are not being called. I have a bam file created using TMAP that I am going to convert to a fastq and realign using bowtie2. Next, I will use bwa on this bam. Does that sound like a goodlan or do you recommend something else? Thank you :).
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