User: irazoqui.matias

Reputation:
10
Status:
New User
Location:
Last seen:
1 year, 6 months ago
Joined:
5 years, 6 months ago
Email:
i**************@gmail.com

about me

Posts by irazoqui.matias

<prev • 7 results • page 1 of 1 • next >
1
vote
2
answers
629
views
2
answers
Answer: A: Batch Download Enzymes by EC Number
... I found a way to do with BASH: while read line; do wget "http://www.uniprot.org/uniprot/?sort=&desc=&compress=no&query="$line"&fil=&format=fasta&force=yes" done < "list.txt" But I don't know if there's another, more efficient way to do it ...
written 18 months ago by irazoqui.matias10
1
vote
2
answers
629
views
2
answers
Batch Download Enzymes by EC Number
... Hi, I have many lists of EC numbers, that look like this: ec:1.13.11.1; ec:1.14.12.10; ec:1.14.12.13; ec:1.14.13.50; ec:1.21.1.2; ec:1.3.1.25; ec:1.3.1.32; ec:3.1.1.45; ec:3.5.5.6; ec:3.8.1.7; ec:4.2.1.84; ec:5.5.1.1; ec:5.5.1.7; ec:6.2.1.33 And I'd like to download all the corresponding sequences ...
ec number sequence uniprot written 18 months ago by irazoqui.matias10
0
votes
1
answer
880
views
1
answers
Comment: C: Alternatives to EUtils to get Taxa from GenBank
... I didn't know about the prot.accession2taxid file, it was just what i wanted ...
written 2.4 years ago by irazoqui.matias10
1
vote
1
answer
880
views
1
answer
Alternatives to EUtils to get Taxa from GenBank
... Hello. I have several files (>200) with more than 100 protein sequences each and I want to get the taxonomy of each sequence. My first thought was using BLAST. Since they are quite a few, I used a PERL scrip to "remote blast" them and then extracted the accession of the best hit. I've tried usin ...
ncbi taxonomy eutils genbank written 2.4 years ago by irazoqui.matias10 • updated 2.4 years ago by Sej Modha4.1k
0
votes
0
answers
691
views
0
answers
Get Reads from a Bin
... Hi, I've got a series of bins (fasta files) obtained with MetaBAT. Each file has all the contigs that were binned together. My question is if there's any way to extract the reads (from the FastQ file) mapped to each of the contigs in a bin. I have the bam mapping files. My idea is to reassemble ...
binning samtools metagenomics written 2.5 years ago by irazoqui.matias10
0
votes
1
answer
1.4k
views
1
answers
Comment: C: Parsing a Megan (RMA) File
... Thanks Charles for replying. Yes, I have the 16S sequences and I've already used QIIME. But now I'm working on the WGS reads and I wanted to do another taxonomical analysis (beacuse by using 16S, you leave behind viruses and eukaryotas). That's why I tried MEGAN. For the BLAST part, I used DIAMOND, ...
written 2.7 years ago by irazoqui.matias10
0
votes
1
answer
1.4k
views
1
answer
Parsing a Megan (RMA) File
... Hi, I having a problem with MEGAN 5. I'm working with some quite large RMA files (40 Gb aprox), built using the trimmed reads and a blast run. The problem is that my (poor little) PC always hangs up when I try to open them. So, I was wondering if there's a way to parse a file via Megan command line ...
bioinformatics metagenomics megan written 2.7 years ago by irazoqui.matias10 • updated 2.7 years ago by Charles Warden6.4k

Latest awards to irazoqui.matias

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: 1196 users visited in the last hour