Ruolin Liu

``` >7001174F:HCY5TBCX3200721:HCY5TBCX3:1:2202:11382:19258 0 19 39964932 51 7S8M1I77M * 0 0 CCCAGCCCCCAGCCCACAGCCCNCAGAGCTACCACCAGGTGGCGCCAAGCCCAGCAGGCTACCAGAATACCCACTCCCCAGCCAGCTACCACC IIIIIIHIIHIIGIIIIIIIIIFIIIIIIHHHCDIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIHHHIIIIIIIIIIHHIIIGIIIIIIII NM:i:2 ms:i:153 AS:i:153 nn:i:1 tp:A:P cm:i:8 s1:i:55 s2:i:0 de:f:0.0233 rl:i:0 Ref+: 1 CCCAGCCC-CAGCCCcCAGAGCTACCACCAGGTGGCGCCAAGCCCAGCAGGCTACCAGAATACCCACTCCCCAGCCAGCT 79 |||||||| |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Qry51:...

Thank you very much for the great tutorial on BW and FM! This is a great read. I think this is a type on Page 10, section 4, the third...

exclude secondary alignment and have mapq cutoff

4

Hi, it would be nice to exclude secondary alignment by default. Thanks.

pro scan context_length = 9 failed, shorter `-c` induces systematic errors

4

Hello, I am using `pro` to scan homopolymer sites. When I increase the context length from 5(default) to 9, the homopolymer A results from *_all got dropped. When I use...

dotplot order by tstart

1

First of all, thanks for writing this nice tool. I think it will be nice if the dotplot can also be ordered by `tstart` since people usually map assembly to...

toil-vg construct fails at building the GBWT index if you haven't specially specified --vcf_phasing files

1

require(len(options.vcf_phasing) > 0, 'generating a GBWT requires a VCF with phasing information'). After delete `_phasing` it works again.

When use multiple thread, the assembled_transcripts.gtf is not sorted correctly.