Zhu xitong comments

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                                            Zhu xitong

something wrong in bedtools getfasta -name

It's true that the -name function has been changed since 2.26.0. The output is not same like what said in the getfasta doc: ``` $ cat test.fa >chr1 AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG $...

get_coverage_filter: blast filter cutoff

@luca-Wang Sorry for the very late reply. I am busy with some other projects. Now I have some time to update ppsPCP. We use _and_ to ensue high confidence of...

Error when run the example data!!!

Sorry for a late reply. Have you checked your perl version? Or the bedtools getfasta command in the ppsPCP.sh file to use -fo as output instead of standout. Several months...

Use of uninitialized value in concatenation (.) or string at /home/wangzt/software/ppsPCP/bin/../src/get_the_pav_seq.pl line 33, <LI> line 6170.

Probably because a higher version of bedtools was used during the run. Version 2.25.0 should avoid this problem, as well as another one where only Ns were added in the...

Bio::Root::Exception <<Bad end parameter (270015). End must be less than the total length of sequence (total=160554)

@Github-Yilei Do you finally fix it? This error rarely happens.

Bio::Root::Exception <<Bad end parameter (270015). End must be less than the total length of sequence (total=160554)

OK, @Github-Yilei I will check it once I am free.

error when run example!

Sorry for a late reply. This peoblem shoud derive from that bedtools getfasta bug. I downloaded it very long time ago and I could use standout as output, like *bedtools...

Call SNPs and INDELs from last results

Hi, @mcfrith, really thanks for you timely reply. I roughly read the tools you have posted above and found maffilter can be used to call SNPs only and seems other...

Custom genomes

Hi, @stianlagstad, Thanks for your suggestions in great details. During last week, I tried to modify those source codes, but I could only make get_circle working by creating a fake...