User: pyjiang2

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pyjiang230
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New User
Location:
United States
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1 month, 1 week ago
Joined:
3 years, 9 months ago
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Posts by pyjiang2

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Where can I get ?or how can I make a mappability track for hg38 assembly
... Thanks! It is indeed memory issue!! ...
written 6 weeks ago by pyjiang230
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Comment: C: Where can I get ?or how can I make a mappability track for hg38 assembly
... Weirdly, the `gemtools index` command works for me, but not `gem-indexer` (as in the wiki). However, when I run gem-mappability, it gives me this error: ```Loading index (likely to take long)...Illegal instruction (core dumped)``` I don't know what is the wrong here. ...
written 7 weeks ago by pyjiang230
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Answer: A: GEM index fatal error
... I encountered the same problem here, and I found another thread in this post which I found useful: https://www.biostars.org/p/181014/ rather than using `gem-indexer`, use `gemtools index`, which do not throw that error message to me. [still running now] ------ Well, although I get passed the inde ...
written 7 weeks ago by pyjiang230
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Comment: C: How To Convert A Genome Mappability Data (Gem-Mappability) To Ucsc Compatible Fo
... I found many of the above links don't work. Maybe there's a change in their website. I found this useful post which includes steps to generate wig file, which steps follow Sheila's description. https://wiki.bits.vib.be/index.php/Create_a_mappability_track ...
written 7 weeks ago by pyjiang230
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How does variant callers deal with N in the reference sequence?
... If there is an N in the reference genome, after the variant calling pipeline, if an alternative base (A/T/G/C) is called at the same position, will it be output in the VCF? Or any variants with the N in the reference will be ignored? Thanks! ...
genome reference N variant call written 6 months ago by pyjiang230 • updated 6 months ago by JC7.0k
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Comment: C: Error reading gff file into R (with read.gff from the ape package)
... I encountered the same problem. It is because there are fasta files at the end. Try `grep -n ">" gff_file` to find the fasta files, and then just take the lines before that into a new file which won't give this error. ...
written 9 months ago by pyjiang230
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Answer: A: How to split vcf file by chromosome?
... You can use vcftools. For example, if total 16 chromosomes for i in {1..16}; do vcftools --vcf VCF_FILE --chr $i --recode --recode-INFO-all --out VCF_$i; done ...
written 9 months ago by pyjiang230
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Comment: C: Change output name for ADMIXTURE analysis
... I've run into the same problem! It is very annoying when I run multiple jobs on cluster and I just notice it today. ...
written 9 months ago by pyjiang230
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Answer: A: How To Remove The Same Sequences In The Fasta Files?
... I tried fastx_collapser first, but it gives error for multiple aligned fasta sequences.   I found this useful website, which gives unique fasta sequences and concatenate the header name for the same sequences as well: http://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/fasta/uniqueseq. ...
written 3.7 years ago by pyjiang230
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bcftool merge -r ?
... Hi everyone, I have individual vcf files of indels and want to merge them into a big one, but only extract chromosome 3,4,5,7,8 into a unified file. The list of vcf files is in round1_indel.txt.  What I did is:  bcftools merge -l round1_indel.txt -o round1_indel.vcf  -r 3,4,5,7,8 However, the ou ...
vcf bcftool written 3.7 years ago by pyjiang230 • updated 3.6 years ago by Biostar ♦♦ 20

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Popular Question 5 months ago, created a question with more than 1,000 views. For bcftool merge -r ?
Supporter 6 months ago, voted at least 25 times.

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