User: vebaev

gravatar for vebaev
vebaev130
Reputation:
130
Status:
Trusted
Location:
Last seen:
4 months, 3 weeks ago
Joined:
3 years, 3 months ago
Email:
v*****@plantgene.eu

Posts by vebaev

<prev • 128 results • page 1 of 13 • next >
0
votes
1
answer
366
views
1
answer
Compare 2 BAM files for covarage regions
... Hi, Is there a way to compare two BAM files for a difference in coverage and extract regions (giving GFF) which differs? (I'm mapping small RNAs) i.e. extracting regions with the different expression. ...
bam bigwig covarage deeptools gff written 6 months ago by vebaev130 • updated 6 months ago by Jennifer Hillman Jackson25k
0
votes
1
answer
269
views
1
answers
Comment: C: Help with an simple workflow (annotation)?
... As my thoughts are cleared, I need a way to convert a table blast result to GFF so I can intersect it with the genome GFF for annotation purposes? Is there such tool? ...
written 6 months ago by vebaev130
0
votes
2
answers
178
views
2
answers
Answer: A: Tools for annotating unknown sequences?
... I want to annotate plant sequences of unsequenced genome, in other words, to see my sequences to what they are similar in NCBI. ...
written 6 months ago by vebaev130
0
votes
1
answer
269
views
1
answer
Help with an simple workflow (annotation)?
... Dear all, I need a recommendation about what tools to use in a workflow for annotation of sequences. Basically, I have contigs I have to map and annotate in a genome and get results each contig from which region comes (GFF on the genome is provided also along fasta)? ...
local galaxy annotation written 6 months ago by vebaev130 • updated 6 months ago by Jennifer Hillman Jackson25k
0
votes
2
answers
178
views
2
answers
Tools for annotating unknown sequences?
... Dear all, what tools are there in the toolshed suitable to annotate 1000 sequences? (is there a way blasting them remotely to NCBI and summarizing like retrieving the top result for each query)? ...
local galaxy annotation written 6 months ago by vebaev130
2
votes
1
answer
341
views
1
answer
Sample order in Deseq2?
... Hi, are the right order in Deseq2 is first "treated" and second "control" to produce changed expression in the treated sample? Thanks! ...
expression deseq2 rna-seq de differential written 10 months ago by vebaev130 • updated 10 months ago by Jennifer Hillman Jackson25k
0
votes
1
answer
640
views
1
answers
Comment: C: Docker Galaxy Job conf file and SLURM
... I'm using Docker-Galaxy v17, and I'm using it without any change in the job_conf files right now. So probably any of the tools uses 1 CPU at the moment. I would like to make it so I can use more cores. ...
written 10 months ago by vebaev130
0
votes
1
answer
640
views
1
answers
Comment: C: Docker Galaxy Job conf file and SLURM
... Hi, can you share your job_conf file since I want to setup our docker-galaxy also to use more than 1 cpu? I see you have succeeded. ...
written 10 months ago by vebaev130
0
votes
1
answer
1.2k
views
1
answers
Comment: C: How to upload Mouse reference genome mm10, in Fasta format to My Galaxy History
... In this regard can you directly five FASTA GZIP (.fa.gz) file to Galaxy and then feed the data manager or the genome should be unzipped first (local galaxy)? ...
written 11 months ago by vebaev130
0
votes
1
answer
329
views
1
answers
Comment: C: Tool working on Galaxy v17 but give error on Galaxy v16
... Strange, I have upgraded my Galaxy to the latest v17, and the error persists. How is possible to add the missing distribution from the error manually or somehow fix this? ...
written 11 months ago by vebaev130

Latest awards to vebaev

Popular Question 9 months ago, created a question with more than 1,000 views. For Unable to fetch .......[Errno 28] No space left on device (Galaxy in Docker)
Popular Question 19 months ago, created a question with more than 1,000 views. For Unable to fetch .......[Errno 28] No space left on device (Galaxy in Docker)
Popular Question 19 months ago, created a question with more than 1,000 views. For Galaxy via Docker?
Popular Question 19 months ago, created a question with more than 1,000 views. For Mapping quality plot of BAM file
Centurion 20 months ago, created 100 posts.
Supporter 20 months ago, voted at least 25 times.
Popular Question 21 months ago, created a question with more than 1,000 views. For Human annotation GFF suitable for Galaxy Cufflinks (hg38)?
Rising Star 3.2 years ago, created 50 posts within first three months of joining.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 157 users visited in the last hour