User: Ati

gravatar for Ati
Ati30
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30
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8 months, 1 week ago
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4 years, 7 months ago
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Posts by Ati

<prev • 49 results • page 1 of 5 • next >
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Comment: C: Bam output of deduplication using UMItools
... The question is adjusted. What do you mean? The reads need to be aligned first for the deduplication using UMItools! ...
written 8 months ago by Ati30
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Bam output of deduplication using UMItools
... I have paired RNA-seq data with high duplication rate. My reads contain UMI so after aligning with `STAR`, I run `umitools dedup` with `--paired` option. I would expect that the output bam file would have an equal number of read1 and read2 (output of `samtools flagstat`). I'm a bit confused with th ...
samtools flagstat dedup umitools rna-seq bam written 8 months ago by Ati30
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Comment: C: High number of reads with the incorrect strand designation.
... That's now clear to me! Thank you! ...
written 8 months ago by Ati30
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Comment: C: memory problem runnig multiqc --interactive
... Thank you very much! Yes, it is a memory problem but I couldn't yet solve it! Of course, it worked without `--interactive` option but as I have many samples having an interactive plot will be better. ...
written 8 months ago by Ati30
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memory problem runnig multiqc --interactive
... I got the following error when I use the --interactive command option of multiqc. Traceback (most recent call last): File "/usr/local/bin/multiqc", line 766, in multiqc() File "/usr/local/lib/python3.6/site-packages/click/core.py", line 764, in __call__ return self.main(*args, ...
rna-seq multiqc written 8 months ago by Ati30 • updated 8 months ago by genomax89k
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Comment: C: High number of reads with the incorrect strand designation.
... Thanks! As my data is paired I have specified `STRAND=SECOND_READ_TRANSCRIPTION_STRAND`. That's why I'm a bit surprise with the results! ...
written 8 months ago by Ati30
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Comment: C: High number of reads with the incorrect strand designation.
... I'm not sure about the exact kit but it was a stranded RNA-seq library prep kit. ...
written 8 months ago by Ati30
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High number of reads with the incorrect strand designation.
... I have used `CollectRnaSeqMetrics` to check the numbers of reads with the correct/incorrect strand designation. The results showed that more than 80% of reads in almost all of the samples are mapped to the incorrect strand! What would be a good explanation for these results? Thank you in advance! ...
picard rna-seq collectrnaseqmetrics written 8 months ago by Ati30
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Comment: C: Deduplication using UMItools
... Thank you for your help! ...
written 8 months ago by Ati30
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Comment: C: Deduplication using UMItools
... @Devon Ryan Thank you! Even if the UMI length is short (5bp)? ...
written 8 months ago by Ati30

Latest awards to Ati

Great Question 19 months ago, created a question with more than 5,000 views. For how to download gene annotation bed file from ensembl?
Great Question 3.8 years ago, created a question with more than 5,000 views. For Bed to BedGraph
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Popular Question 3.8 years ago, created a question with more than 1,000 views. For how to download gene annotation bed file from ensembl?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For How to download intronic positions from Ensembl
Popular Question 3.8 years ago, created a question with more than 1,000 views. For How to annotate positions using biomaRt R package?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Convert ensembl gene ID
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Bed to BedGraph

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