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skip orientation FF/RF/RR by bwa mem

Hi everyone

I extracted DNA fragments from human somatic tissue, sequenced them, and then try to align data to the ref genome (hg38) using bwa mem. But bwa mem always skipped orientation (FF/RF/RR). Other posts also reflect such questions, but they all have the following "as there are not enough pairs by bwa mem" hints. My alignments were just "skip orientation FF skip orientation RF skip orientation RR". However, I can still get a whole bunch of sam file, so I just wonder whether these skips matters or not?

Thanks a lot 

bwa mem -q hg38.fa unknown_circle_reads_1.fastq unknown_circle_reads_2.fastq > unknown_circle.sam
alignment
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updated by ATpoint ATpoint • written by 14301010010 • 14301010010

here is the head of raw sequencing data @A00582:345:HFVCWDSXY:2:1101:1506:1094 1:N:0:CGTACTAG+TAGATCGC CAATTAAAACTGACTACAAAAAGAAAATATTGCATTGTAAAATAATAAAAGCATGTAAATGCTTTATAAATTTTATAGGCTATTTTCTGAGTAACTTTCCCATGATTCCCCGGTTCTGTGCTATATGGTAGCATTGCTGGAACCGGAAGT + :F,FFFFFFFFFFF,F:F:FFFF:FF:FF:FF,,FFFFFF:,FFFFFF:F::FFFF:FFFFFF:FFF:FF,FFFFFFF:FFFFF:F:FFFFF,FFFFF,:FFFFFFF,,FF:FFF:FF:,,,FFFFFFFFF,:FF,FF:,:F:,FF::,F @A00582:345:HFVCWDSXY:2:1101:3152:1094 1:N:0:CGTACTAG+TAGATCGC GTGAAGAGCTGCATTAGGAATCTTAAGGTGGAGGTTGGGGTAGGTGGCTTGAGCTGTCTCTTATACACATCTCCCAGCCCACGAGACCGTACTAGATCGCGTATGCCGTCGTCTTCGTGCACAGGGGGGGGGGGGGGGGGGGGGGGGGGG + FFF:FF,FFFFFFFFFFFFFFFF:FFFF::FFF,:FFF,F,FFFFFFFFFFFFFFF:FFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:FF,FFFFFFF,FFFFFF,FFFF,:,,,,,:,,:,,,,:FFFFFFFFFFFFFFFFFFFFFFFF @A00582:345:HFVCWDSXY:2:1101:4562:1094 1:N:0:CGTACTAG+TAGATCGC GGATTAGAGGCAGTGATCTACACATTCATTAAAGAAGCATTGAAGTAAATTATGAATCCCGTGATGCATATTGAATCTGTCTCTTATACACATCTCCGAGCCCACGAGACCGTACTAGATCTCGTAAGCCGTCTTCTGCGTGAAAAGGGG

And here is the head of hints https://ibb.co/4TgrMSz

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written by 14301010010 • 14301010010

1 answer

These are just the normal (internal) status messages with which bwa spams the screen, ignore them.

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written by ATpoint ATpoint

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