User: cvu
cvu • 90
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Posts by cvu
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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 9 days ago by
cvu • 90
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... Thanks for the reply microfuge ...
written 10 days ago by
cvu • 90
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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 10 days ago by
cvu • 90
• updated
9 days ago by
Samuel Brady • 220
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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 ...
written 11 days ago by
cvu • 90
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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 5 weeks ago by
cvu • 90
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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 9 weeks ago by
cvu • 90
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141
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... thanks a lot genomax. I tried `bbmerge.sh` but got same result. ...
written 9 weeks ago by
cvu • 90
2
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... Hello people,
I've paired end 16s metagenomic data. I tried to join forward and reverse reads with `join_paired_ends.py` but 50% data was assembled and I'm loosing 50% of my data which comes in `fastqjoin.un1.fastq` and `fastqjoin.un2.fastq`. I think my reads are not overlapping there must be gap b ...
written 9 weeks ago by
cvu • 90
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Comment:
C: htseq read count zero ?
... Thanks a lot Carlo Yague. I changed `-a 5` and number of read count increased. ...
written 9 weeks ago by
cvu • 90
0
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1
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137
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Comment:
C: htseq read count zero ?
... thanks Devon. I have not filtered my Trinity output !! May be that's one of the reasons. ...
written 9 weeks ago by
cvu • 90
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