User: cvu
cvu • 180
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Posts by cvu
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... You can use `sed` command if you just want to remove these characters
`sed 's/[N|?|-]//g' filename` ...
written 2.4 years ago by
cvu • 180
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... Hello All,
I've created a bowtie2 large index, Which is a huge data set (~100GB) it took approx 2days to generate a bowtie2 index. Now I came across problems with some sequences and I want to remove it from my existing index.
Is there a way to remove sequences based on their identifiers directly ...
written 2.4 years ago by
cvu • 180
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... Did you resolve this problem? which OrgDb can be used? ...
written 3.0 years ago by
cvu • 180
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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 3.2 years ago by
cvu • 180
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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 3.5 years ago by
cvu • 180
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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 3.5 years ago by
cvu • 180
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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 3.6 years ago by
cvu • 180
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... Thanks for the reply microfuge ...
written 3.6 years ago by
cvu • 180
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