BWA and BAM to FASTQ

Hello, I converted bam files to fastq using samtools and then ran bwa alignment with this fastq file, but it did not complete it showed some errors like "paired reads have different names: "A00728:385:HC3F7DRXY:1:2165:24822:14043", "A00728:385:HC3F7DRXY:1:2138:9191:5854".

Thank you

bam fastq bwa

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updated 7 months ago by Ram

• written 2.6 years ago by qudrat.nii •

1 answer

Did you collate or name sort the BAM files before doing the conversion? Also selected only primarily aligned reads?

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written 2.6 years ago by GenoMax

I did not sort bam files and did not select primary alignment

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written 2.6 years ago by qudrat.nii •

Then please do that.

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written 2.6 years ago by GenoMax

Thank you, it worked

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written 2.6 years ago by qudrat.nii •

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