User: vmicrobio

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vmicrobio250
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Posts by vmicrobio

<prev • 105 results • page 1 of 11 • next >
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Answer: A: how to get a readable scale on a particular R plot
... It was recommanded to me to use `pheatmap` package (https://stackoverflow.com/questions/63225729/how-to-get-a-readable-scale-on-a-particular-r-plot) Here is what I get: install.packages("pheatmap") library(pheatmap) # load data and subset data=read.table("/Users/vmicrobio/Des ...
written 4 days ago by vmicrobio250
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Comment: C: how to get a readable scale on a particular R plot
... thank you for your comment. `tmp.100` is a 15x87 table (including one line and one column of headers). Without `trim.heatmap` I get the same graph. ...
written 16 days ago by vmicrobio250
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how to get a readable scale on a particular R plot
... Hello, I'm having difficulties to get a plot with a readable scale. I have plotted transcriptomic data using R with package EMA. However 'genes names' (ordinate axis) are written too big and I can't see all gene names. I would like to have one gene name per compartment. [plot picture][1] H ...
R ema transcriptomic plot written 16 days ago by vmicrobio250
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Answer: A: how to highlight hotspot rearrangments regions?
... It seems that the best way is to try different SV callers and compare results. I found an interesting comparative list of softs (Guan and Sung, Methods, 2016) : [1]https://ibb.co/Zhky3Hn [1]: https://ibb.co/Zhky3Hn ...
written 5 months ago by vmicrobio250
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Answer: A: Contig longer than mitochondrial sequence. Explanation ?
... You may have some similar patterns in your mitochondrial which will generate errors during assembly. What de novo assembler did you used? which parameters? You may try more stringent parameters or another software ...
written 6 months ago by vmicrobio250
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how to highlight hotspot rearrangments regions?
... Hello biostars community I would like to understand what happened in a human genome containing some complex rearrangements. I would like first to focus on a/some region/s containing potentially rearrangements and then look deep at the hybrid reads present in this particular region. However there a ...
hybrid reads rearrangment hotspot region written 6 months ago by vmicrobio250
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Comment: C: count number of references with at least one hit
... and `wc -l` output file ...
written 8 months ago by vmicrobio250
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Comment: C: count number of references with at least one hit
... I had to format a little bit the heads of multifasta file but it works. Thanks a lot! ...
written 8 months ago by vmicrobio250
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Comment: C: count number of references with at least one hit
... I just would like to get the information : on X references Y are mapped by at least one read. Do you think I should go with idxstats output? ...
written 8 months ago by vmicrobio250
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count number of references with at least one hit
... Hello, In a context of mapping reads with multireferences, I was wondering how to count number of references with at least one hit (and not number of reads matching with ref). A way would be to make a custom script with files obtain from `samtools idxstats` after alignment. Is there a `samtools` c ...
alignment references written 8 months ago by vmicrobio250 • updated 8 months ago by Pierre Lindenbaum129k

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