Would the bowtie2 option `--no-unal` cause an issue ?

[Louis-MG]

Hello ! I have alignments against scaffolds batches of 300 samples. The sam files are pretty big (15G) and the conversion to bam files causes an error due to the error:

[E::bam_hdr_write] Header too long for BAM format

I have th efollowing propositions to reduce the file size:

• remove headers of unmapped reads
• removing secondary alignments (I fear this could impact SemiBin2 a lot)

Can I apply these ideas ?

[Louis-MG]

Nevermind, I finally figured out that the vast majority of my scaffolds have a length <=2500bp, I filtered them and that dramatically reduces the size of everything. I am still curious about the secondary alignments though.