User: opplatek

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opplatek60
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https://janbio.home.blog/
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jan_oppelt
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Posts by opplatek

<prev • 20 results • page 1 of 2 • next >
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Comment: C: qualimap reported java.awt.AWTError: Can't connect to X11 window server
... The link is no longer active. [Here][1] is an updated link for the same thing. [1]: http://qualimap.conesalab.org/doc_html/faq.html#x11problem ...
written 5 weeks ago by opplatek60
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Comment: C: Gene set enrichment analysis with logFC and PValue
... In DESeq2, `stat` is very similar to this metric. A simple plot of DESeq2 `stat` vs your metric: ![DESeq2 stat vs metric][1]. X-axis is `stat` from DESeq2 Bioconductor R package and y-axis is the metric calculated as you described. Some more details can be found [here][2] and in DESeq2 [vignette][ ...
written 7 weeks ago by opplatek60
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Comment: C: Creating gtf file?
... What do you need a gtf for and what kind of information do you think it should contain? Since you have transcriptome assembly, a gtf in your case could be only used to describe CDS region and you already have that in the `longest_orfs.gff3`. The situation would be different if you had an assembled g ...
written 7 weeks ago by opplatek60
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Answer: A: How to convert realign BAM file into fastq file
... Based on the other comments `samtools fixmate` didn't help so it seems you have some singleton reads (reads without a mate). That the most likely cause of BWA failing afterward. To synchronize them back (=remove singleton reads) You can also use `repair.sh` from BBMap. For more information, you can ...
written 7 weeks ago by opplatek60
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Comment: C: How to convert realign BAM file into fastq file
... You obviously lost some of the mates during your processing. My guess is that one of the steps you've used filtered out one of the mates but kept the other one. Without having the whole code it's impossible to know where they got lost. And since it seems you don't have any of the previous BAMs you w ...
written 7 weeks ago by opplatek60
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Answer: A: Unlisting lists inside data frame and collapsing their values in R
... If you don't want to use `for` loop you can just use a combination of `apply` (to iterate over columns) and `sapply` (to iterate over lists). # Apply to all columns apply(myDataFrame, 2, function(y) sapply(y, function(x) paste(unlist(x), collapse=":"))) # Apply to all columns but ...
written 7 weeks ago by opplatek60
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Comment: C: Getting transcriptomic coordinates for CDS exons from a GTF
... Possible duplicate of https://www.biostars.org/p/251076/ and https://www.biostars.org/p/230758/ ...
written 8 weeks ago by opplatek60
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Answer: A: How to use Rsamtools to extracting reads map into single chromosome from BAM fil
... [Rsamtools][1] manual suggests how to handle big bam files (section 2.1 Large bam files). Basically, you can use `which` option for in `ScanBamParam` to limit the loaded regions. From here, you can use something like this to load one whole chromosome at the time: loadChr <- function(seqname, ...
written 3 months ago by opplatek60
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Answer: A: Convert BLAT to GFF file?
... [This][1] works fine. [1]: http://eugenes.org/gmod/tandy/blat2gff.pl ...
written 13 months ago by opplatek60
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Comment: C: How Can I Know The Length Of Mapped Reads From Bam File?
... The `bam2bed` will fail if you have spliced alignments. But he didn't specify if DNA or RNA alignment in the question so the answer is still valid. ...
written 17 months ago by opplatek60

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Supporter 7 months ago, voted at least 25 times.

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