User: Ambika

gravatar for Ambika
Ambika30
Reputation:
30
Status:
New User
Location:
United States/Auburn/Auburn University
Last seen:
22 hours ago
Joined:
2 years, 7 months ago
Email:
a***************@gmail.com

Posts by Ambika

<prev • 96 results • page 1 of 10 • next >
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Interpreting co-ordinates file
... 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 ...
genome alignment written 4 months ago by Ambika30 • updated 4 months ago by Mensur Dlakic4.3k
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Mummer for running multiple query files
... 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 ...
assembly mummer alignment nucmer written 4 months ago by Ambika30
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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 9 months ago by Ambika30
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how to download cazy database
... 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 ...
database cazymes written 9 months ago by Ambika30 • updated 9 months ago by Dattatray Mongad350
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Comment: C: Remove double vertical bar "||" at the end of the sequence in a fasta file
... Thanks you so much it works. ...
written 9 months ago by Ambika30
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Remove double vertical bar "||" at the end of the sequence in a fasta file
... 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 ...
fasta sed awk written 9 months ago by Ambika30 • updated 9 months ago by SMK1.9k
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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 9 months ago by Ambika30
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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 9 months ago by Ambika30
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Parsing a fasta file
... Hello everyone, I have a fasta file like this in multiple lines >jgi|Necha2|9923|gw1.3.792.1 CGTGGCCAGGCTCTTTATATTCGCTCACTCTTCGAGGCCAACCGCAATGTGACTGATCCGAGACACCAAA GAGCTCTGTTGACGGAGACAGAGAAGCTACTGGAGAGCTGGAAGCACCCCGATCCCTACACGCCCCCGAC TGCTCCCGGAGGCTCAAAGTTCGAGCGAAACCTGCCATCG ...
assembly sequence written 9 months ago by Ambika30
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Comment: C: qPCR: Huge variation in fold change of genes between biological replicates
... @Kevin I am just using cDNA to amplify the genes. I did not apply any whole genome amplification ...
written 21 months ago by Ambika30

Latest awards to Ambika

Great Question 4 months ago, created a question with more than 5,000 views. For Unable to access jarfile trimmomatic-0.35
Popular Question 4 months ago, created a question with more than 1,000 views. For Interpretation of Results from trimmomatic
Popular Question 4 months ago, created a question with more than 1,000 views. For HTseq Pysam error
Popular Question 4 months ago, created a question with more than 1,000 views. For stranded vs not stranded Htseq-output differences
Popular Question 4 months ago, created a question with more than 1,000 views. For HTseq error: Too few arguements
Popular Question 8 months ago, created a question with more than 1,000 views. For Cufflinks gtf file to htseq
Popular Question 8 months ago, created a question with more than 1,000 views. For DESeq2 workflow for RNAseq
Supporter 9 months ago, voted at least 25 times.
Popular Question 21 months ago, created a question with more than 1,000 views. For Deseq2 library load error
Popular Question 21 months ago, created a question with more than 1,000 views. For Unable to access jarfile trimmomatic-0.35
Popular Question 21 months ago, created a question with more than 1,000 views. For HTseq Pysam error
Popular Question 21 months ago, created a question with more than 1,000 views. For Trimmomatic jar file
Popular Question 21 months ago, created a question with more than 1,000 views. For Interpretation of Results from trimmomatic
Popular Question 21 months ago, created a question with more than 1,000 views. For HTseq error: Too few arguements
Popular Question 21 months ago, created a question with more than 1,000 views. For DESeq2 workflow for RNAseq
Popular Question 21 months ago, created a question with more than 1,000 views. For Feature Counts output interpretation
Popular Question 23 months ago, created a question with more than 1,000 views. For Unable to access jarfile trimmomatic-0.35
Rising Star 2.4 years ago, created 50 posts within first three months of joining.

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