User: michael.ante
michael.ante • 3.3k
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Posts by michael.ante
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Answer:
A: hisat2-build half done
... Wheat has a huge genome. With STAR I needed more than 145 GB memory and some tricks as described in several post to reduce the Index size.
I don't know what memory footprint Hisat2 is producing, but I guess you have similar memory requirements.
Cheers,
Michael ...
written 9 weeks ago by
michael.ante • 3.3k
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... Hi msimmer92,
Currently, I'm not 100% into this topic. I think it would be best to post this as a new question referring to this thread. I can remember that there are two ways of structuring a wig file, but which way is the more appropriate one I cannot remember.
Best,
Michael ...
written 11 weeks ago by
michael.ante • 3.3k
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... done, was just c&p-ing ...
written 12 weeks ago by
michael.ante • 3.3k
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... Hi oussriradnane,
What I see in your posted coed is that the `--with-gsl` option is missing. As far as I understand it, you need to run `./configure --with-gsl /path/to/gsl` .
Cheers,
Michael
[edit formating] ...
written 12 weeks ago by
michael.ante • 3.3k
• updated
12 weeks ago by
genomax ♦ 70k
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... As a small addition, do a fastQC report for each sample before and after trimming. Afterwards, run on the reports the multiqc tool.
Then you'll see the differences in adapter content, read length, etc.
...
written 3 months ago by
michael.ante • 3.3k
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... [RSeQC][1]offers a variety of graphics for alignment QC. Some of the tabular output files can afterwards be nicely visualised using [multiQC][2].
[1]: http://rseqc.sourceforge.net
[2]: http://multiQC.info ...
written 3 months ago by
michael.ante • 3.3k
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... Hi Hellocita,
I mean that the genes which are not protein coding genes, (especially the two you mentioned in your questions) are off-targets of the polyA-enrichment. Your oligo-dT primer has a certain length and might bind to intrinsic A-rich regions of certain transcripts. The enrichment of these ...
written 3 months ago by
michael.ante • 3.3k
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... Hi Hellocita,
Both genes you mentioned have a A-rich region at the cDNA's 3' site (e.g. [ENSG00000257155 / ENST00000548096][1]). Therefore, the polyA fishing / enrichment can result in reads from these transcripts.
I guess you did nothing wrong.
Regarding of keeping these genes in your analysis ...
written 3 months ago by
michael.ante • 3.3k
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... Your reads are mapped against entities which are like "`fig|6666666.35312.peg.1`". HTSeq-count is looking for exon covering reads which are located at entries with the name "`scaffold-0`". Since there is no overlap, HTSeq is reporting only "`__no_features`".
You need either to map against the genom ...
written 4 months ago by
michael.ante • 3.3k
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... You mapped apparently against the transcritome, since the mapping position in the bam file corresponds to the gene I'd of your annotation file. ...
written 4 months ago by
michael.ante • 3.3k
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For C: Merge 2 files based on rs number but keep all info only from the first file
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For C: Merge 2 files based on rs number but keep all info only from the first file
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For A: questions on rna-seq data analysis
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For C: Merge 2 files based on rs number but keep all info only from the first file
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