User: pendragon

gravatar for pendragon
pendragon50
Reputation:
50
Status:
New User
Location:
Last seen:
3 years, 5 months ago
Joined:
4 years, 2 months ago
Email:
c******************@gmail.com

Posts by pendragon

<prev • 14 results • page 1 of 2 • next >
1
vote
0
answers
1.5k
views
0
answers
MUMmer-NUCmer error message
... Hi, I'm working with two mouse olfactory organ transcriptome datasets of the same mouse species, but sequenced and assembled using different methods. I wanted to use MUMmer to perform an alignment of the transcriptomes to start to assess the different methods. I tried using NUCmer (which seemed the ...
software error alignment written 3.8 years ago by pendragon50
1
vote
0
answers
2.9k
views
0
answers
Renaming fasta file headers
... I have large fasta files containing all the sequences of some large families of receptors, each sequence is currently indicated by the ensembl ID. I would like to change each ensembl ID header to be the gene ID. I have a list of all the corresponding IDs (ensembl - gene), is there a way to change th ...
fasta rename headers written 4.2 years ago by pendragon50 • updated 4.2 years ago by genomax91k
1
vote
2
answers
5.5k
views
2
answers
Comment: C: Retrieve a subset of FASTA from large Illumina multi-FASTA file
... Thank you so much, really appreciate all the help! It works great using filterbyname.sh :) ...
written 4.2 years ago by pendragon50
0
votes
2
answers
5.5k
views
2
answers
Comment: C: Retrieve a subset of FASTA from large Illumina multi-FASTA file
... I know I now have to entire ID name and using seqtk is also producing emtpy files, so I thought maybe it was the same issue. If I find some other reason it's happening I'll let you know. Thanks for the help! ...
written 4.2 years ago by pendragon50
0
votes
2
answers
5.5k
views
2
answers
Comment: C: Retrieve a subset of FASTA from large Illumina multi-FASTA file
... Would the presence of "/" in the names also cause a problem with seqtk, if I had the full names (such as the two example IDs below) in the txt file? >c13667/f1p2/1252 isoform=c13667;full_length_coverage=1;non_full_length_coverage=2;isoform_length=1252 >c2819/f1p4/3296 isoform=c2819;full_lengt ...
written 4.2 years ago by pendragon50
0
votes
2
answers
5.5k
views
2
answers
Comment: C: Retrieve a subset of FASTA from large Illumina multi-FASTA file
... I’ve run into some problems using BBmap My list in my txt file looks like:(isoseq.8.16.IDs.txt) c10984/f1p0/1692 c8658/f1p0/1429 c3671/f1p0/1618 c11188/f1p0/1685 The actual IDs contain more information and look like:(polished_high_qv_consensus_isoforms.8.16.fasta) >c ...
written 4.2 years ago by pendragon50 • updated 4.2 years ago by genomax91k
0
votes
2
answers
5.5k
views
2
answers
Comment: C: Retrieve a subset of FASTA from large Illumina multi-FASTA file
... So the code entered looks like this: cd seqtk export PATH=/workdir/spretus.vno/seqtk:$PATH seqtk subseq mouse.refseq.fasta vmnr.txt > VRs.fasta The VRs.fasta file is created but is empty. The list of IDs in the text file look like the list below but much longer: ENSMUSG0000008 ...
written 4.2 years ago by pendragon50 • updated 4.2 years ago by genomax91k
0
votes
2
answers
5.5k
views
2
answers
Comment: C: Retrieve a subset of FASTA from large Illumina multi-FASTA file
... It seems to be working, however the output file which should contain all the sequences I want is empty. My only idea is that the list of IDs only has the Ensembl gene names, but the sequences in the fasta file have both the gene and transcript IDs. Would that prevent seqtk from successfully searchin ...
written 4.2 years ago by pendragon50
0
votes
2
answers
5.5k
views
2
answers
Comment: C: Retrieve a subset of FASTA from large Illumina multi-FASTA file
... Yes I'm trying to extract a set of receptor sequences (whose names I have specified in a txt file, each unique ID occupying a single line) from the mouse refseq database. So I had thought that using the seqtk subseq command would work ...
written 4.2 years ago by pendragon50
0
votes
2
answers
5.5k
views
2
answers
Comment: C: Retrieve a subset of FASTA from large Illumina multi-FASTA file
... I get usage info, the version, and a list of commands to use with short definitions ...
written 4.2 years ago by pendragon50

Latest awards to pendragon

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1892 users visited in the last hour