User: al-ash

gravatar for al-ash
al-ash0
Reputation:
0
Status:
New User
Last seen:
3 days, 8 hours ago
Joined:
2 years, 4 months ago
Email:
b*********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by al-ash

<prev • 30 results • page 1 of 3 • next >
0
votes
1
answer
1.3k
views
1
answers
Comment: C: Reduce saturation by deleting the 3rd position in each codon of DNA seqs. R ape
... I might not understand the command `AlignmentToFilter[, -seq(1, ncol(AlignmentToFilter), by=3) ]` .. but it is apparently skipping the first codon position in my hand while command `AlignmentToFilter[, -seq(3, ncol(AlignmentToFilter), by=3) ]` worked for me and omitted the 3rd codon position. ...
written 15 days ago by al-ash0
0
votes
2
answers
4.1k
views
2
answers
Answer: A: Deleting The 3Rd Codon Position In A Multiple Sequence Alignment And Substitutio
... For deleting 3rd codon position using R, see a related Q&A on biostars: [Reduce saturation by deleting the 3rd position in each codon of DNA seqs. R ape package][1] [1]: https://www.biostars.org/p/132801/ ...
written 16 days ago by al-ash0
0
votes
4
answers
2.3k
views
4
answers
Answer: A: Filtering Msa For Phylogenetic Tree Construction
... I suggest to check [this article][1] on the benefits of MSA filtering for subsequent phylogeny reconstruction - you might decide not to filter at all after reading it :) [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538881/ ...
written 10 weeks ago by al-ash0
0
votes
10
answers
33k
views
10
answers
Comment: C: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
... Please note that by default the sequence header extracted by pyfaidx is truncated on first whitespace. ...
written 12 weeks ago by al-ash0
0
votes
10
answers
33k
views
10
answers
Comment: C: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
... I have the same question - does samtools faidx support regular expression/wildcards? (as I'm using samtools faidx in some of my previous scripts I'd prefer to stay with it rather than migrating to the python faidx) ...
written 12 weeks ago by al-ash0
0
votes
0
answers
274
views
0
answers
OrthoDB - How to retrieve ortholog groups for only the selected species
... I'm using JSON API to retrieve from OrthoDB ortholog cluster ids for which genes are present in the selected species (e.g. Blatella germanica and Zootermopsis nevadensis), but apparently the retrieval is not limited with the argument `species=6973%2C136037` which I'm using; rather it retrieves all ...
api json ortholog orthodb written 6 months ago by al-ash0
0
votes
8
answers
50k
views
8
answers
Answer: A: How to download raw sequence data from GEO/SRA
... Note that it might be necessary to convert the *.sra to *.fastq using some special parametres supplied to `fastq-dump` to make it suitable for Trinity assembly (to take care of the read names), i.e. for paired reads: SRA_TOOLKIT/fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files file.sra ...
written 7 months ago by al-ash0
0
votes
1
answer
398
views
1
answers
Comment: C: "Optimal" setting of CPU and max_memory in Trinity
... Ok, I did not realize that limiting the RAM might be because of not completely draining the machine - this makes sense. Thanks for clarification. Since we touched this topic, I'm actually wondering - what if I set CPUs exceding the actual number of available CPUs? Would you expect some drop in tri ...
written 7 months ago by al-ash0
0
votes
1
answer
398
views
1
answers
Comment: C: "Optimal" setting of CPU and max_memory in Trinity
... Yes, but I'm not really sure whether it means, that the optimal performance will be reached when I set the max_memory as close to the expected peak RAM requirement as possible...I'm still wondering what effect will have if I set, for example, the max_memory much higher than required according to the ...
written 7 months ago by al-ash0
1
vote
1
answer
398
views
1
answer
"Optimal" setting of CPU and max_memory in Trinity
... I'm wondering if there is any guideline (or and advice from experienced user) on the `--CPU` and `--max_memory` parametres in Trinity (v2.3). Will suboptimal setting of these parametred dramatically influence the computational time? E.g. I'm running assembly of 10M illumina paired reads (from insec ...
trinity ram cpu written 7 months ago by al-ash0 • updated 5 months ago by euduca0

Latest awards to al-ash

Popular Question 22 days ago, created a question with more than 1,000 views. For How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
Supporter 5 weeks ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 657 users visited in the last hour