Moderator: lakhujanivijay
lakhujanivijay ♦ 4.7k
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Bioinformatics 💻 Programmer | Linux ❤ Lover | Constant ☕ Learner
A passionate bioinformatician interested in developing solutions for analyzing, visualizing and integrating clinical and research data.
Me = ( ¼ Bioinformatician ) + ( ¼ Programmer ) + ( ½ Biologist )
Let's connect !
Find me on ORCID
https://orcid.org/0000-0002-6529-0841Posts by lakhujanivijay
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... What have you tried so far? Please do not expect ready made answers. ...
written 2 days ago by
lakhujanivijay ♦ 4.7k
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Comment:
C: converting taxID to taxonomy
... Did you try [taxonkit][1]
[1]: https://bioinf.shenwei.me/taxonkit/usage/ ...
written 3 days ago by
lakhujanivijay ♦ 4.7k
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... https://www.biostars.org/u/41746/ I did not get you. ...
written 4 weeks ago by
lakhujanivijay ♦ 4.7k
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... Hi All
I am interested in calling consensus genotype for few germline samples using BAM files as initial inputs. The CGES (Consensus Genotyper for Exome Sequencing) [paper][1] describes a workflow where they have integrated 4 different variant callers - GATK, samtools, FreeBayes and Atlas-SNP-2.
W ...
written 4 weeks ago by
lakhujanivijay ♦ 4.7k
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Comment:
C: How to assemble contigs?
... Thanks for sharing this information https://www.biostars.org/u/30/ ...
written 4 weeks ago by
lakhujanivijay ♦ 4.7k
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... I am trying to run DepthOfCoverage from GATK3 (it's an old - no more supported version) which requires RefSeq file , however, that files contains all transcripts and not just canonical transcript. I was wondering how can I generate that file. ...
written 6 weeks ago by
lakhujanivijay ♦ 4.7k
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...
From the UCSC genome browser, is there any way to download *knownCanonical* set from the **NCBI Refseq** track as it is possible for the **UCSC** track (see screenshot below)
*knownCanonical* is not available in the dropdown in **table** option when we select **NCBI Refseq**
...
written 6 weeks ago by
lakhujanivijay ♦ 4.7k
• updated
4 weeks ago by
jnavarr5 • 10
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Answer:
A: What do you think of sci-hub?
... Looks like almost everyone across the world us using scihub
Source : [Who's downloading pirated papers? Everyone][1]
[1]: https://www.sciencemag.org/news/2016/04/whos-downloading-pirated-papers-everyone ...
written 7 weeks ago by
lakhujanivijay ♦ 4.7k
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... You can try [CopyNumberPlots][1]
[1]: http://www.bioconductor.org/packages/devel/bioc/vignettes/CopyNumberPlots/inst/doc/CopyNumberPlots.html ...
written 7 weeks ago by
lakhujanivijay ♦ 4.7k
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... Hi Jyotika,
> [1] I have the read file and assembled contigs (both in .fasta format)
Reads in fasta? Are you sure its not fastq rather?
> [2] I need to calculate the coverage for each single contigs across the read file
This does not make sense . What do you mean by *across the read file*? ...
written 8 weeks ago by
lakhujanivijay ♦ 4.7k
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