User: pyjiang2

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pyjiang220
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1 month ago
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Posts by pyjiang2

<prev • 6 results • page 1 of 1 • next >
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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 5 weeks ago by pyjiang220 • updated 5 weeks ago by JC6.8k
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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 4 months ago by pyjiang220
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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 4 months ago by pyjiang220
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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 4 months ago by pyjiang220
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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 3.3 years ago by pyjiang220
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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 3.4 years ago by pyjiang220 • updated 3.2 years ago by Biostar ♦♦ 20

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