User: cvu
cvu • 110
- Reputation:
- 110
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- India
- Last seen:
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Posts by cvu
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... Did you resolve this problem? which OrgDb can be used? ...
written 5 months ago by
cvu • 110
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... Hi all,
I've performed fisherTests() function of bsseq bioconductor package for two samples since I've only one replicate for each samples. but fishertest result gives only two columns p.value and log2OR and I want to know its corresponding chromosome and position information. also I want to filter ...
written 7 months ago by
cvu • 110
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... Hello All,
I am running Bisulfide sequencing samples. I've directional libraries with four single-ended fastq files for each sample and completed with bismark and got four bam files which i've merged and finally got one bam file for each sample.
These are the commands I ran:
bismark --genome_ ...
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Comment:
C: standalone BLAST parametes
... Thanks for the reply. I want only one best match for each protein, Hence I set hsp 1. ...
written 11 months 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 11 months ago by
cvu • 110
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1
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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 13 months ago by
cvu • 110
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478
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... Thanks for the reply microfuge ...
written 13 months ago by
cvu • 110
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479
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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 13 months ago by
cvu • 110
• updated
13 months ago by
Samuel Brady • 240
3
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478
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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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