User: cvu
cvu • 110
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Posts by cvu
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C: standalone BLAST parametes
... Thanks for the reply. I want only one best match for each protein, Hence I set hsp 1. ...
written 4 days ago by
cvu • 110
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Comment:
C: standalone BLAST parametes
... Thanks for the reply. I want perfect matches, but which parameters to set to get a good match? ...
written 4 days ago by
cvu • 110
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... Hi All,
I've predicted genes in genome. Now I want to identify proteins, For that, I've blasted all predicted proteins against uniprot database.
blast parameters
blastp -query proteins.fasta -db Uniprotdb -max_target_seqs 1 -max_hsps 1 -out output.blastp -outfmt 6 -evalue 0.001
what should b ...
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... use SRA Toolkit https://www.ncbi.nlm.nih.gov/books/NBK158900/ and use fastq-dump, for example `fastq-dump -I --split-files SRR390728` to split paired end reads. ...
written 8 weeks ago by
cvu • 110
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... Thanks for the reply microfuge ...
written 9 weeks ago by
cvu • 110
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... Hello all,
I want to filter variants based on their genomic location.
For example RSID rs10863805, this variant is Intronic variant and it is 18 nucleotides away from exon and I want to keep all intronic variants which falls in before or after 100 nucleotides of exon region.
> 5'-------INTRON ...
written 9 weeks ago by
cvu • 110
• updated
8 weeks ago by
Samuel Brady • 230
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... Hi All,
I'm using PLAAC (http://plaac.wi.mit.edu/) to identify probable prion subsequences in my protein sequences.
but I get different LLR scores for same protein sequence, when I give fasta and multifasta files.
Output from FASTA file
SEQid MW MWstart MWend MWlen LLR LLRstar ...
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... Hello People,
I am new to RAD-seq analysis and I've 100 samples of RAD-seq paired end double digest data from single population. I ran ipyrad and have got different output formats (vcf, loci, geno, phy, str etc.). Now I'm not able to generate graphs. I want to do qtl mapping, parsimony analysis, ph ...
written 12 weeks ago by
cvu • 110
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... can I put Ns between two reads to link them? it is 2x250 reads, and insert length is approximately 420. ...
written 3 months ago by
cvu • 110
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213
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... thanks a lot genomax. I tried `bbmerge.sh` but got same result. ...
written 3 months ago by
cvu • 110
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