User: michael.ante

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michael.ante3.3k
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Posts by michael.ante

<prev • 364 results • page 1 of 37 • next >
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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.ante3.3k
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Comment: C: Converstion of BED with scores into bigWig
... 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.ante3.3k
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Comment: C: mash configure error --with-gsl can not find gsl
... done, was just c&p-ing ...
written 12 weeks ago by michael.ante3.3k
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Answer: A: mash configure error --with-gsl can not find gsl
... 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.ante3.3k • updated 12 weeks ago by genomax70k
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Comment: C: General question about batch effect, read trimming and what to do when the adapt
... 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.ante3.3k
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Answer: A: How to visualize bam, bed and vcf files programmatically using Python and Shell
... [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.ante3.3k
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Comment: C: should non-protein-coding rna(e.g. lncRNA) be removed in RNA-Seq differential ex
... 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.ante3.3k
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Answer: A: should non-protein-coding rna(e.g. lncRNA) be removed in RNA-Seq differential ex
... 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.ante3.3k
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Comment: C: HTSeq & featureCounts show no features
... 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.ante3.3k
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Comment: C: HTSeq & featureCounts show no features
... 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.ante3.3k

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Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Can FPKM be added?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Can FPKM be added?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: insert word in each row
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Merge 2 files based on rs number but keep all info only from the first file
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: insert word in each row
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Scholar 7 months ago, created an answer that has been accepted. For A: questions on rna-seq data analysis
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: insert word in each row
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Scholar 17 months ago, created an answer that has been accepted. For A: questions on rna-seq data analysis
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: Merge 2 files based on rs number but keep all info only from the first file
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: insert word in each row
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: Merge 2 files based on rs number but keep all info only from the first file
Scholar 19 months ago, created an answer that has been accepted. For A: questions on rna-seq data analysis
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