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Recent Replies
Comment: absolute path for symbolic links in Snakefile
by
Jesse
▴
770
That's really handy, and much more of a general solution than stripping off the directory names! So yifangt86, if you're on Linux you can …
Comment: Truncated metadata file report from ENA Portal API
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GenoMax
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Are you missing a `"` at the end of the URL. Doing
wget -O test.out "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=PRJNA43…
Comment: Different output for read length
by
marco.barr
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100
very strange, I double checked the BAM file and it is the same one I used for your request. Are the commands I wrote above correct? How is …
Comment: Different output for read length
by
Pierre Lindenbaum
161k
the first read as a length of 1747, i wonder how you can just find '50'
$ wget -qO - "https://gist.githubusercontent.com/Macdot3/4650…
Comment: Problem with Seurat package in PercentageFeatureSet function
by
bk11
★
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Yes, `CreateAssayObject` function is used for only expression matrix.
Comment: Different output for read length
by
marco.barr
▴
100
Here is my result, I hope you can see it.
[https://gist.github.com/Macdot3/4650243a10540d8c06f728ffc16a136c][1]
[1]: https://gist.gith…
Comment: Different output for read length
by
marco.barr
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I just published my link on paste, why can't I see my public paste on the site?
Comment: cellranger error message
by
Max
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0
I'm having a similar issue. The sample_id matches the filename prefix before _S1_L001, but I get the error:
Log message:
Requested sample(s…
Comment: Different output for read length
by
marco.barr
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Thanks so much GenoMax, I'm sharing the link as you told me
Comment: Different output for read length
by
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Post the data at pastebin.com and add a link here or you could a GitHub gist. You were suspended by biostars SPAM bot since you pasted link…
Comment: Different output for read length
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GenoMax
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Post the data at pastebin.com and add the link here. You were suspended by biostars SPAM bot since you pasted these links in quick successi…
Comment: RNA seq analysis
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Could you clarify on what exactly you are referring to with "SRA data table". If you are retrieving fastq files (raw data), then you could …
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
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sovrappensiero
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Thanks, Chris. I really appreciate your help. This has clarified a lot for me!
Answer: Snakemake fails to find conda in PBS
by
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Snakemake does not have support for micromamba. There is an open issue: https://github.com/snakemake/snakemake/issues/2322
Comment: absolute path for symbolic links in Snakefile
by
tim.booth
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Further to this answer - if you are using GNU coreutils (ie. any modern Linux), there is a "-r" flag to fix this problem. I typically use "…
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