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Phil Ewels
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Jeremy Leipzig
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Recent Replies
Answer: How do I extract references from ClinVar for all variants in individual gene?
by
Pierre Lindenbaum
155k
get a bed file for your genes and use tabix:
tabix --regions genes.bed "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar…
Comment: How to write a Python program that takes the sequences.fasta file and writes N s
by
Pierre Lindenbaum
155k
https://www.biostars.org/p/76716/ ; https://www.biostars.org/p/9461227/ ; https://www.biostars.org/p/105388/; https://www.biostars.org/p/38…
Comment: Trying to use hmmer to search genes over metagenome assembled genomes
by
Mensur Dlakic
★
23k
It is nice that you posted this to give this question a closure, but this is far from an optimal procedure. `esl-translate` is also not a g…
Answer: Trying to use hmmer to search genes over metagenome assembled genomes
by
v.berriosfarias
▴
130
I finally solved this with the help of the hmmer devs https://github.com/EddyRivasLab/hmmer/issues/302#issuecomment-1539968198
Firstly yo…
Comment: multiqc: group samples by population + boxplot ?
by
Phil Ewels
★
1.2k
Yes the documentation for Custom Content is the worst out of all MultiQC docs. I've been intending to rewrite it for a while now. Best bet …
Comment: Is there a file format better suited for the era of pangenomics than the .vcf? W
by
Jeremy Leipzig
21k
> "Explicit representation: VCF is very explicit about the exact type
> and sequence of variation"
no, tinyliar, it isn't - ambiguous repr…
Comment: Why some insertions are symbolic in ALT column?
by
Maxine
•
0
sounds great! waiting for your findings~
Comment: Why some insertions are symbolic in ALT column?
by
Maxine
•
0
thank you for sharing your experience!
Comment: What are your preferred programs for processing DNA long reads? (de novo assembl
by
Medhat
9.6k
There is already an article about the topic that was recently published (I was one of the individuals approached to contribute to this arti…
Comment: Is there a file format better suited for the era of pangenomics than the .vcf? W
by
Vincent Laufer
★
3.0k
Apologies - my email address and twitter are listed on my profile page.
Comment: multiqc: group samples by population + boxplot ?
by
Pierre Lindenbaum
155k
It worked by parsing a first run of multiqc, extract the data from the sanitised data , create a SVG plot with R, include the SVG into a fi…
Comment: Solving environment: failed with initial frozen solve. Retrying with flexible so
by
Ahmed
▴
10
thanks, bro I get the solve of my problem by installing new environment and reinstalling samtools software again.
Comment: Solving environment: failed with initial frozen solve. Retrying with flexible so
by
Ahmed
▴
10
Thanks for telling me that, and i apologize for bad explanation because I am beginner user with the site!
Comment: amrfinder not working on loop?
by
Pierre Lindenbaum
155k
what is the output of the following commands:
ls -lah '/home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta'
…
Comment: amrfinder not working on loop?
by
GenoMax
130k
> Cannot open file
> '/home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta'
Looks like either the file path is in…
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