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Recent Replies
Comment: How can I find KO IDs for ORF sequences from kofam_scan ?
by
Nikesh
•
0
Thank you, I changed it as #SBATCH --time=1-00:00:00 and it's running. I will keep you updated and thanks again.
Comment: Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads
by
aeb
▴
20
Thanks for your input. I read STAR is generally not meant to align to the transcriptome and there would be other more optimized ways to do …
Comment: Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads
by
aeb
▴
20
Thanks for your response! I understand the cost difference may not be much... I am considering to compare this approach to just aligning to…
Answer: How can I find KO IDs for ORF sequences from kofam_scan ?
by
Mensur Dlakic
★
29k
Already answered in your other post.
I suggest you inquire about the SLURM time limit and set it to a maximum value allowed. This would …
Comment: How can I find KO IDs for ORF sequences in a large FASTA file?
by
Mensur Dlakic
★
29k
What @genomax said. I suggest you inquire about the SLURM time limit and set it to a maximum value allowed. This would be 6 days:
#SBA…
Comment: How can I find KO IDs for ORF sequences from kofam_scan ?
by
Nikesh
•
0
This is one of sequence;
>k127_52915239_12 # 4220 # 5476 # -1 # ID=1511550_12;partial=00;start_type=ATG;rbs_motif=TAAA;rbs_spacer=11bp;gc_…
Comment: How can I find KO IDs for ORF sequences from kofam_scan ?
by
GenoMax
151k
Looking at the command line you used and the manual for kofam_scan, multi-threading should be in use. How long are your query sequences?
…
Comment: How can I find KO IDs for ORF sequences from kofam_scan ?
by
Nikesh
•
0
The same error is occurring. I’m wondering if parallel processing is not being utilized during the execution.
Answer: How can I find KO IDs for ORF sequences from kofam_scan ?
by
GenoMax
151k
Please don't post the same content in multiple places.
> I tried changing differenet cpu allocation too.
As I wrote in the other comment…
Comment: How can I find KO IDs for ORF sequences in a large FASTA file?
by
GenoMax
151k
> JOB 10654468 ON c2023 CANCELLED AT 2025-06-10T21:46:45 DUE TO TIME LIMIT *”
You are asking for one minute less than 6 hours in your SLUR…
Comment: How can I find KO IDs for ORF sequences in a large FASTA file?
by
Nikesh
•
0
@mensur
Hi,
I set up the environment in HCC, and my FASTA file contains 98 sequences. This is my SLURM script, but I’ve tried running it …
Comment: Significant reads loss after fastp
by
AIMAR
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10
Hi, concerning your read size in your command you've specified to keep reads with a minimum length of 50 bp with the option `--length_requi…
Answer: Isoform analysis after quantification with Salmon/Star
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The following papers show the advantages of Salmon with Gibbs resampling, followed by edgeR's catchSalmon, glmQLFit, glmQLFTest (for DTE) a…
Comment: Significant reads loss after fastp
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What kind of data is this? Changing default parameters for programs should be done based on an understanding of the characteristics of your…
Comment: Significant reads loss after fastp
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Shazel
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Thanks for the reply. The experiment cannot be run again so I need to proceed with this data. It would be helpful if you could give me an i…
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