User: msobol

gravatar for msobol
msobol20
Reputation:
20
Status:
New User
Location:
Last seen:
3 months, 1 week ago
Joined:
1 year, 5 months ago
Email:
m*****@islander.tamucc.edu

Posts by msobol

<prev • 51 results • page 1 of 6 • next >
0
votes
1
answer
259
views
1
answers
Comment: C: Redirecting pHMMER output to /dev/null
... I don't have much experience in using programming languages to create scripts, but I will see what I can find. Thanks for the advice! ...
written 4 months ago by msobol20
0
votes
1
answer
259
views
1
answers
Comment: C: Redirecting pHMMER output to /dev/null
... The developer of hmmer recommended that I use head -4 in conjunction with /dev/null. Unfortunately, what I need is just the top hit per-query basis and I don't have the skills to create a script to do this. I wonder why hmmer does not have the option to output just one hit per a query like blast al ...
written 4 months ago by msobol20
0
votes
1
answer
259
views
1
answers
Comment: C: Redirecting pHMMER output to /dev/null
... I edited my original question with what the tbl file looks like in Excel. I want one hit for each gene, but instead I am getting several 100 to 1000 hits for each query. ...
written 4 months ago by msobol20
0
votes
1
answer
259
views
1
answers
Comment: C: Redirecting pHMMER output to /dev/null
... Unfortunately, it did not work. My tbl output still looks the same. :/ I am kind of at a lost... ...
written 4 months ago by msobol20
0
votes
1
answer
259
views
1
answers
Comment: C: Redirecting pHMMER output to /dev/null
... Yes, I thought that the .tbl and the output were the same file since I was using --tblout . That is correct, I wanted the results file to only include the top hit from each gene. When I was contacting the developer, what he said/what I understood was to discard the main output to /dev/null, save a ...
written 4 months ago by msobol20
0
votes
1
answer
259
views
1
answers
Comment: C: Redirecting pHMMER output to /dev/null
... Thanks for your help, I understand now what you are saying about the differences in stdout and stderr but how does this script only give me the top hit for each of my queries? Wouldn't I need to add something like head -4, to tell it to throw everything out of the stderr that isn't the top hit? Whe ...
written 4 months ago by msobol20
0
votes
1
answer
259
views
1
answers
Comment: C: Redirecting pHMMER output to /dev/null
... So would it look this? i.e do I have the 2>&1 in the correct position? Do I keep or remove the ; after null? (/dev/null; ....) phmmer --tblout 1371E_merops5.tbl /work/Geomicrobiology/msobol/IODP_329_SPG/1371E14H2/maker/1371E_uni_snap.maker.output/1371E_uni_snap.renamed.maker.proteins.fas ...
written 4 months ago by msobol20
0
votes
1
answer
259
views
1
answers
Comment: C: Redirecting pHMMER output to /dev/null
... I am just directing the output to .tbl only using --tblout [Before][1] [After][2] [1]: https://photos.google.com/photo/AF1QipMDyZmjICO4WVPF6-OoOyOkRP01cSI9AdwOp74Q [2]: https://photos.google.com/photo/AF1QipPj_Yu4RJQSzLk6TCVJSuiQUE2T0b3yRFflK6tz [3]: https://photos.google.com/photo/AF1Qip ...
written 4 months ago by msobol20
10
votes
1
answer
259
views
1
answer
Redirecting pHMMER output to /dev/null
... Hey guys, Something that should be so simple has been so difficult for me to resolve the past few weeks. I am using pHMMER to search my ~12,000 fungal gene predictions against the MEROPS database. The issue is that for some of my gene queries, over a 1,000 hits will be returned, making it impossib ...
gene annotation hmmer protein genome written 4 months ago by msobol20
0
votes
0
answers
650
views
0
answers
Comment: A: Ran dipSpades for a diploid fungus genome -- now what?
... Hi OP, Did you ever figure out what was best to do? I feel stuck after doing genome annotation with MAKER. I used the consensus_contigs.fasta file for downstream analysis, but I am not sure if this is the right file to have proceeded with. I feel like there are a lot of duplicated genes reported ...
written 5 months ago by msobol20

Latest awards to msobol

Popular Question 4 months ago, created a question with more than 1,000 views. For To reassemble Illumina and PacBio, or just upgrade previous assembly with PacBio?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1520 users visited in the last hour