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Recent Replies
Comment: Different output for read length
by
marco.barr
▴
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
★
2.4k
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
▴
100
I just published my link on paste, why can't I see my public paste on the site?
Comment: cellranger error message
by
Max
•
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
▴
100
Thanks so much GenoMax, I'm sharing the link as you told me
Comment: Different output for read length
by
GenoMax
142k
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
by
GenoMax
142k
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
by
s.ghazala
•
0
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
by
sovrappensiero
▴
100
Thanks, Chris. I really appreciate your help. This has clarified a lot for me!
Answer: Snakemake fails to find conda in PBS
by
tim.booth
▴
50
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
▴
50
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 "…
Answer: Different output for read length
by
Pierre Lindenbaum
161k
I supect your reads are hard clipped. Show us the first lines of
samtools view /home/sorted.bam | cut -f 2,6,10 | head -n 20
Comment: Presence of unknown sites in ANNOVAR output file
by
sainavyav22
•
0
Here you go.
1.perl convert2annovar.pl -format vcf4old 1008_Tumor.vcf > 1008Tumor_variant.avinput
2.perl annotate_variation.pl 100…
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