skrakau / sim_iclip Goto Github PK

Hi, first of all a big thanks for providing all data & code - makes reproducing super easy! 👍

In the wiki you discard read1 with following command:

samtools view -hb -f 630 rna-seq.bam -o rna-seq.R2.bam

This outputs an empty bam file for me. Is 630 a typo?

If I am not mistaken these are the selected flags:

• 1 0x1 template having multiple segments in sequencing
• 2 0x2 each segment properly aligned according to the aligner
• 4 0x4 segment unmapped
• 8 0x8 next segment in the template unmapped
• 16 0x10 SEQ being reverse complemented
• 32 0x20 SEQ of the next segment in the template being reverse complemented
• 64 0x40 the first segment in the template
• 128 0x80 the last segment in the template
• 256 0x100 secondary alignment
• 512 0x200 not passing filters, such as platform/vendor quality controls
• 1024 0x400 PCR or optical duplicate
• 2048 0x800 supplementary alignment

Thanks a lot! :-)