BWA and BAM to FASTQ

Question

[qudrat.nii]

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

Answer 1

[GenoMax]

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

[qudrat.nii]

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

[GenoMax]

Then please do that.

[qudrat.nii]

Thank you, it worked