User: pyjiang2
pyjiang2 • 30
- Reputation:
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- 1 month, 1 week ago
- Joined:
- 3 years, 9 months ago
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Posts by pyjiang2
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... Thanks! It is indeed memory issue!! ...
written 6 weeks ago by
pyjiang2 • 30
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... 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
pyjiang2 • 30
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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
pyjiang2 • 30
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... 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
pyjiang2 • 30
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... 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! ...
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... 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
pyjiang2 • 30
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... 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
pyjiang2 • 30
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... 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
pyjiang2 • 30
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... 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
pyjiang2 • 30
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... 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 ...
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