User: Ambika
Ambika • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- United States/Auburn/Auburn University
- Last seen:
- 4 weeks ago
- Joined:
- 2 years, 3 months ago
- Email:
- a***************@gmail.com
Posts by Ambika
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... Hello everyone,
I got the coordinate file after aligning my query genome file to the reference genome file using MUMmer. Now I want to distinguish core and accessory genome using that coordinate file. But I do not know how I can do that. The coordinate file looks like this:
[S1] [E ...
written 28 days ago by
Ambika • 30
• updated
28 days ago by
Mensur Dlakic • 2.5k
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84
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... Hello everyone,
I am trying to use Mummer to differentiate core and accessory chromosomes in some genome assembly files I have. I used the following code to align single query file to the single reference file which seems to work fine.
nucmer -maxmatch -c 100 -p Fop Fol_fasta Fusox.fasta
...
written 4 weeks ago by
Ambika • 30
0
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1
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Comment:
C: how to download cazy database
... @Dattatray I was following the link on their paper. I did not know they moved it. Now it works. Thanks a lot. ...
written 5 months ago by
Ambika • 30
3
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1
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290
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1
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... Hey Biostars,
I am trying to download [Cazy][1] database, but I could not find a place where I can download. I also tried another program [dbcan][2] but the site they provided does not seem to open.
Thank you,
Ambika
[1]: http://www.cazy.org/
[2]: http://cys.bios.niu.edu/dbCAN2 ...
written 5 months ago by
Ambika • 30
• updated
5 months ago by
Dattatray Mongad • 340
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4
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... Thanks you so much it works. ...
written 5 months ago by
Ambika • 30
21
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4
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289
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7 follow
4
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... Hello I have a fasta file as
>jgi|FusspF23_1|104542
GGTTCTCTTGTCTGTTTTTAAAAGAGTCTCGAGACCCC||
>jgi|FusspF23_1|10121
GGGGCCGCCCTCGATTCATCAGCGAAATTGCTCAGTCGGGCG||
at the end of fasta sequence I have these symbols `"||"` which I want to remove. I tried using *sed* but in that wa ...
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211
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Comment:
C: Parsing a fasta file
... I think I figure it out with the sed command. I just replaced the space that I had with that output.fa file with a line using this code.
sed 's/\t/\n/g' output.fa> output1.fa
>jgi|Necha2|9923|gw1.3.792.1
CGTGGCCAGGCTCTTTATATTCGCTCACTCTTCGAGGCCAACCGCAATGTGACTGATCCGAGACACCAAAGAGCT ...
written 5 months ago by
Ambika • 30
0
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211
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Comment:
C: Parsing a fasta file
...
I tried this awk command
awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < input_best_transcripts.fasta > output.fa
It gives me the fasta file with single line
>jgi|Necha2|9923|gw1.3.792.1 CGTGGCCAGGCTCTTTATATTCGCT ...
written 5 months ago by
Ambika • 30
0
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0
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211
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0
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... Hello everyone,
I have a fasta file like this in multiple lines
>jgi|Necha2|9923|gw1.3.792.1
CGTGGCCAGGCTCTTTATATTCGCTCACTCTTCGAGGCCAACCGCAATGTGACTGATCCGAGACACCAAA
GAGCTCTGTTGACGGAGACAGAGAAGCTACTGGAGAGCTGGAAGCACCCCGATCCCTACACGCCCCCGAC
TGCTCCCGGAGGCTCAAAGTTCGAGCGAAACCTGCCATCG ...
written 5 months ago by
Ambika • 30
0
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1.0k
views
0
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... @Kevin I am just using cDNA to amplify the genes. I did not apply any whole genome amplification ...
written 17 months ago by
Ambika • 30
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