User: Dineshkumar K
Dineshkumar K • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- Kasaragod, Kerala, India
- Last seen:
- 5 days, 17 hours ago
- Joined:
- 11 months, 1 week ago
- Email:
- d*************@gmail.com
Posts by Dineshkumar K
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... @h.mon, Yes, I have different length sequences in my gene1.fasta file. Can't I concatenated different length alignment file?. Moreover, I have more than 2000 alignment files, so manual curation is tedious to do. Therefore, could you please suggest any other tool, which can serve my purpose. ...
written 7 days ago by
Dineshkumar K • 30
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... I am trying to concatenate `mafft` and `gblock` processed multiple gene alignment files/sequences and make `supermatrix` by using `FASconCAT-G v1.0`, However, I end up with an error as follows,
!FILE-ERROR!: Unequal sequence lengths in file gene1.fasta!
READ IN gene1.fasta
Is there any way to ...
written 7 days ago by
Dineshkumar K • 30
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... Thank you so much `@cpad0112` and @russhh. It works awesome. I ran the following command,
ga@pls:~/Desktop/int/tolc$ parallel './seqkit range -r {}:{} *.fasta -o output/group_{}.fasta' ::: $(seq 1 $(grep -c ">" species1.fasta))
and successfully got results in the output folder, The output i ...
written 7 days ago by
Dineshkumar K • 30
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... Thank you @Joe, It serve my purpose perfectly. ...
written 7 days ago by
Dineshkumar K • 30
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... @ cpad0112
I created a `output` folder and then ran the command as you mentioned, but there is no file has been created in `output` directory. The terminal printed as follows,
ga@pls:~/Desktop/int/tolc$ parallel --dry-run 'seqkit range -r {}:{} *.fasta -o output/group_{}.fasta' ::: $(seq 1 $(gr ...
written 8 days ago by
Dineshkumar K • 30
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... Thank you russhh, for your suggestion. I would try to do the same. ...
written 8 days ago by
Dineshkumar K • 30
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... Thank you @cpad0112. However, it shows error as follows,
ga@pls:~/Documents/data/xap95/ortho_cluster/orthogenes_dna/test$./seqkit range -r {}:{} *.fasta -o output/group_{}.fasta ::: $(seq 1 $(grep -c ">" species1.fasta))
[ERRO] invalid range: {}:{}. type "seqkit range -h" for more examp ...
written 8 days ago by
Dineshkumar K • 30
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2
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156
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Comment:
C: Need help in programming?
... @russhh, Yes, I have the same number of sequences in the two fasta file ( In reality, I have 30 fasta files and each fasta file consist of 3000 sequences in it. I need to extract position wise 1,2,3...3000 sequences from all the 30 fasta file and save in new files like group1.fasta, group2.fasta.... ...
written 8 days ago by
Dineshkumar K • 30
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... I would like to extract sequences consecutively from a large fasta files and save in new fasta files. For example, I have two fasta files namely species1.fasta and species2.fasta as given below,
species1.fasta
>tag1
TGCAAGAG
>amylase
ATCGAGAT
species2.fasta
> ...
written 8 days ago by
Dineshkumar K • 30
• updated
6 days ago by
Chirag Parsania • 1.7k
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... Thank you genomax,
...
written 26 days ago by
Dineshkumar K • 30
Latest awards to Dineshkumar K
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For devtools Installation error in R (version 3.5.3)?
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For How to count the length of fasta sequences?
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