User: bioinformatics.queries
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Posts by bioinformatics.queries
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C: Error in running RSEM
... Thank you so much for your response. ...
written 2 days ago by
bioinformatics.queries • 50
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... Yes the problem was just with the compressed file. Thank you so much. ...
written 4 days ago by
bioinformatics.queries • 50
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... Hi
I was able to run `sortmerna` for filtering `rDNA` from `DNA-sequencing` data. It is required to `unzip` the `fastq` file to run the `sortmerna`. I did take 100 reads and was able to filter out `rDNA` from the sequencing data.
Thanks
...
written 5 days ago by
bioinformatics.queries • 50
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... Thanks you so much for your response. ...
written 7 days ago by
bioinformatics.queries • 50
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... I run the test file and it has been executed as per the suggestion and I have the results attached to this link [test_rna_results][1]. I have also included both `stderr` and `stdout' in the uploaded file. I would like to know if the command was executed correct?
My next question is can we use `sor ...
written 8 days ago by
bioinformatics.queries • 50
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... In answer to your question.
1. I did run on HPC cluster and we use `sbatch` to run the command.
2. I do not know how was it installed.
3. yes the output paths are accessible and writable.
4. I am pointing my `--workdir` to `/data/shilpia2/NOR.sequecnes/temp/`
5. I will work on the test read set. ...
written 8 days ago by
bioinformatics.queries • 50
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... I ran the command as suggested and the log-file was generated. The command stopped after running for 2 days of specified wall time without generating any results. I am looking forward for suggestions ahead. I used 56 processors to run the command. Please find the log-file in the link-below. [log-fi ...
written 9 days ago by
bioinformatics.queries • 50
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... I am so sorry with the screen shot. Please find the link for log file being uploaded. [log-file-sortmerna][1]
[1]: https://gofile.io/d/OKeVCL ...
written 11 days ago by
bioinformatics.queries • 50
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... ![stdout][1]
Here is stdout
[1]: https://i.ibb.co/jzqfnvq/stdout.png ...
written 11 days ago by
bioinformatics.queries • 50
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... Here is stderr
![enter image description here][1]
[1]: https://i.ibb.co/6YYC9Nc/stderr.png ...
written 11 days ago by
bioinformatics.queries • 50
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