User: baurumon

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baurumon10
Reputation:
10
Status:
New User
Location:
Norway
Last seen:
2 days, 13 hours ago
Joined:
7 months ago
Email:
b*******@gmail.com

Posts by baurumon

<prev • 20 results • page 1 of 2 • next >
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Comment: C: Fasta length count format
... i asked my colleague to install seqkit but it going to take time. is there any way to do it with sed or awk? ...
written 27 days ago by baurumon10
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Comment: C: Fasta length count format
... hi genomax, I want head and length column. tr command is printing one after another. sorry for mistake. ...
written 27 days ago by baurumon10
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Fasta length count format
... Hi, i have used `awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' seq.fasta` to count sequence length. How can i get the output in below format. Thanks in advance head ...
sequence written 27 days ago by baurumon10 • updated 27 days ago by kloetzl1.0k
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Comment: C: Fasta extraction from bed file
... thank you very much. ...
written 4 weeks ago by baurumon10
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Comment: C: Fasta extraction from bed file
... Thanks, But will it be the same position that i want? As i understand, this awk will print 12286289 12295912 in this way and then extract fasta. after alignment i found some coordinate in reverse order. then i divided then into another bed file and to extract those position. ...
written 4 weeks ago by baurumon10
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Fasta extraction from bed file
... hello, how can i extract fasta in reverse order. i have bed file where start position is greater than the stop. this could come from reverse strand. How can i extract fasta file from reverse order? NC_037130.1 12295912 12286289 please help me . Thanks in advance ...
alignment written 4 weeks ago by baurumon10 • updated 4 weeks ago by ATpoint22k
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Comment: C: Reciprocal blast commandline
... this issue is solved. thanks ...
written 4 weeks ago by baurumon10
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Comment: C: Reciprocal blast commandline
... i used this command to blast in database blastn -query work.fa -db ~/Blast/ssalar/ssalar -outfmt '6 qseqid sseqid sseq' -out newblast_out -word_size 11 -evalue 1e-5 -num_alignments 1 -num_threads 10 and got output as bellow. As you can see i have several hit for one sequence. how can i filter be ...
written 4 weeks ago by baurumon10
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CFastaReader: Hyphens are invalid and will be ignored around line 288
... ![enter image description here][1] [1]: https://img.techpowerup.org/190813/screenshot-23.png Hi, I am doing reciprocal blast to find ortholog. for that i run i create database and run blastn and retrieve hit sequence fasta through awk 'BEGIN { OFS = "\n" } { print ">"$2, $3 }' blast.out > ...
alignment written 4 weeks ago by baurumon10 • updated 4 weeks ago by Brice Sarver2.9k
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Comment: C: Blastn .XML to FASTA
... thank you for the suggestion ...
written 4 weeks ago by baurumon10

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