Moderator: Vijay Lakhujani
Vijay Lakhujani ♦ 3.2k
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- https://lakhujanivijay...
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- Last seen:
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- 2 years, 12 months ago
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Bioinformatician♦Programmer♦Learner
Howdy!
- I am a bioinformatician with deep interest in Genomics, specially in next generation sequencing techniques (NGS). I enjoy programming and I usually code in
Python,PERL,RandBASH. Programming is so much fun! - I also try to learn technical stuff with the help of MOOCs. I believe the best way to keep yourself updated is to keep learning. I also write sometimes on technical and non technical stuff. You can check out some of my articles on LinkedIn.
- I love making new friends and discussing ideas. Do not hesitate to drop me an email if I could be of some help :)
Let's connect !
Posts by Vijay Lakhujani
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... And what will that information be used for ? ...
written 2 days ago by
Vijay Lakhujani ♦ 3.2k
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Comment:
C: nr protein db
... Hello yaghoub.amraei!
Questions similar to yours can already be found at:
- [Is It Possible To Extract From Ncbi Nr Database Plant Protein Sequences.?][1]
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply ...
written 2 days ago by
Vijay Lakhujani ♦ 3.2k
• updated
2 days ago by
RamRS ♦ 19k
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... https://www.biostars.org/p/309884/ ...
written 2 days ago by
Vijay Lakhujani ♦ 3.2k
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... `gene.txt` is the input file. output is thrown to standard output (stdout) ...
written 2 days ago by
Vijay Lakhujani ♦ 3.2k
1
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... Dear https://www.biostars.org/u/26550/
Sure, give it a try ! If this is helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted.
![Upvote|Bookmark|Accept][1]
[1]: http://i68.tinypic.com/2m2ykjr.png
...
written 2 days ago by
Vijay Lakhujani ♦ 3.2k
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158
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... Super fast and easy using `grep` pattern matching using regex
grep -P '(?<=\*\*gene=)\w+(?=\*\*)' -o gene.txt
where `gene.txt` if your file name
**Output**
NECTIN3
TAGLN3
SMG6
ERICH1
DLGAP2
PPP2R2B
**Explanation**
`-P` Means pattern
`?<=` Left Anchor
`? ...
written 3 days ago by
Vijay Lakhujani ♦ 3.2k
3
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1
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64
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... Ultrafast solution
**toy fasta file**
$ cat fasta.fa
>1
TGTACGTNNATT
>2
TTTAANNTTTNN
>3
NNTT
TTNN
**solution using [seqkit][1]**
seqkit locate -p N+ fasta.fa --gtf -P
**output**
1 SeqKit location 8 9 0 + . gene_id "N+";
2 SeqKit location 6 ...
written 3 days ago by
Vijay Lakhujani ♦ 3.2k
1
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92
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... Hi https://www.biostars.org/u/40156/
That's appears to be difficult because RefSeq NC_001807 is an African (Yoruban) sequence with over 40 variant nucleotides from the rCRS. On July 8, 2009 the sequence [was removed from GenBank][1] as a reference sequence but may be found. The rCRS has a new numbe ...
written 4 days ago by
Vijay Lakhujani ♦ 3.2k
0
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79
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1
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... "EOF marker is absent" refers to the absence of a special empty BGZF block of 28 bytes, which samtools looks for at the end of the data to indicate the BAM file is complete.
**If you see that error, either:**
(a) Your file is somehow truncated or incomplete (Chances are more that this is the issue ...
written 4 days ago by
Vijay Lakhujani ♦ 3.2k
1
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2
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257
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2
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... A similar post
https://www.biostars.org/p/257336/ ...
written 5 days ago by
Vijay Lakhujani ♦ 3.2k
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For Samtools flagstat number of reads do not match actual total number of reads.
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For Error encountered while running stattest from ballgown package
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For Samtools flagstat number of reads do not match actual total number of reads.
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For Samtools flagstat number of reads do not match actual total number of reads.
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For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
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For Samtools flagstat number of reads do not match actual total number of reads.
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