Moderator: lakhujanivijay
lakhujanivijay ♦ 5.1k
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Bioinformatician 💻 | ☕ Programmer
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 !
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https://orcid.org/0000-0002-6529-0841Posts by lakhujanivijay
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Comment:
C: ACMG 59 genes
... see [this][1] article
[1]: https://www.nature.com/articles/s41436-019-0502-5 ...
written 25 days ago by
lakhujanivijay ♦ 5.1k
7
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1
answer
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... > This website is full of maximum unnecessary answers
I don't agree with this. Biostars has been the most accessed and valued resource for bioinformatics.
> few people ask questions instead of providing any clues
Asking questions is important most of the times in scenarios when:
1. The que ...
written 4 weeks ago by
lakhujanivijay ♦ 5.1k
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156
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Comment:
C: Get summary of aligned sequences
... I believe what https://www.biostars.org/u/1767/ meant is to perform clustering of the protein sequences first; i.e. cluster similar protein sequences into clusters that meet a user-defined similarity threshold. This could be achieved using clustering tools such as CD-HIT; have a look [this](http://w ...
written 4 weeks ago by
lakhujanivijay ♦ 5.1k
0
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1
answer
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... Hi https://www.biostars.org/u/17505/
That's a header incompatibility issue and can be resolved by editing your reference fasta file. Here are few suggestions:
1. check the headers of your reference fasta file:
`grep "^>" /home/kumarm/allan-work/RNASEq-alignment/ref_sequence.fa`
2. check the ...
written 9 weeks ago by
lakhujanivijay ♦ 5.1k
0
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4
answers
2.3k
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4
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Answer:
A: fastq to fasta perl
... See a [python script][1] which I wrote sometimes back
[1]: https://raw.githubusercontent.com/lakhujanivijay/Bioinformatics-Problems-Rosalind/master/FastQ_to_fasta_converter/fastq_2_fasta.py ...
written 10 weeks ago by
lakhujanivijay ♦ 5.1k
0
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1
answer
161
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... The supplementary information [here][1] says
> Query our laboratory information management system to retrieve seven
> Picard sequencing quality control metrics for each sample: GCDROPOUT,
> ATDROPOUT, MEANINSERTSIZE, ONBAITVSSELECTED, PCTPFUQREADS,
> PCTTARGETBASES10X, and PCTTARGETBASE ...
written 10 weeks ago by
lakhujanivijay ♦ 5.1k
0
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1
answer
204
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Comment:
C: Biopython vs Python
... If you need to work with the biopython package, you need that. Think it this way, if you have windows OS, do you need microsoft office ? Answer is yes, if you need powerpoint! ...
written 10 weeks ago by
lakhujanivijay ♦ 5.1k
0
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0
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149
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... Thanks https://www.biostars.org/u/18713/
However I am attempting an installation from the scratch, reason being installing a big set of tools (along with GATK). ...
written 11 weeks ago by
lakhujanivijay ♦ 5.1k
0
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0
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149
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answers
... Hi everyone,
I am wondering whether anyone tried installing GATK inside a singularity container. I can see that there is a tutorial on how to install [gatk inside a docker container][1], however, I could not find anything about singularity.
My current approach is to install conda inside my contain ...
written 11 weeks ago by
lakhujanivijay ♦ 5.1k
0
votes
3
answers
164
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3
answers
... using [seqkit][1]
`seqkit replace -p '(.+)' -r '${1}_HTH_7' sample_1.fasta`
[1]: https://bioinf.shenwei.me/seqkit/download/ ...
written 3 months ago by
lakhujanivijay ♦ 5.1k
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