User: vebaev

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vebaev130
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3 years ago
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Posts by vebaev

<prev • 128 results • page 1 of 13 • next >
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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 3 months ago by vebaev130 • updated 3 months ago by Jennifer Hillman Jackson25k
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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 3 months ago by vebaev130
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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 3 months ago by vebaev130
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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 3 months ago by vebaev130 • updated 3 months ago by Jennifer Hillman Jackson25k
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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 3 months ago by vebaev130
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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 7 months ago by vebaev130 • updated 7 months ago by Jennifer Hillman Jackson25k
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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 8 months ago by vebaev130
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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 8 months ago by vebaev130
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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 8 months ago by vebaev130
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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 9 months ago by vebaev130

Latest awards to vebaev

Popular Question 7 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 16 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 16 months ago, created a question with more than 1,000 views. For Galaxy via Docker?
Popular Question 16 months ago, created a question with more than 1,000 views. For Mapping quality plot of BAM file
Centurion 18 months ago, created 100 posts.
Supporter 18 months ago, voted at least 25 times.
Popular Question 18 months ago, created a question with more than 1,000 views. For Human annotation GFF suitable for Galaxy Cufflinks (hg38)?
Rising Star 3.0 years ago, created 50 posts within first three months of joining.

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