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Comment: Is it appropriate to include singleton reads with paired-end datasets for low-co
by
GenoMax
152k
> I want to make the most of the data
While that desire is understandable, mixing single and paired-end reads is not something all progra…
Answer: DGE analysis in Seurat using paired samples per donor ?
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yura.grabovska
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If all you're interested in doing is doing tumour vs non-tumour from 5 cases then why not create a pseudobulk and just run normal DESeq2 on…
Answer: RNA-seq: TPM batch effect correction
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i.sudbery
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I'm with @rfran010 here. If you're goal is to compare genes within samples, then since all measurements from within a sample come from the …
Comment: Need help using ExpansionHunter
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GenoMax
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> Should I use my Crai or FastQ files as a reference file? Can I produce a reference file from those?
No you can't do that. You will have …
Comment: MACS3 Parameter adjustments
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Thanks, I have used the options `--keep-dup = all` and `--keep-dup = 1`, without previously performing a filter process with samtools or P…
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Did you specify the temporary directory? If it's not specified, the directory points to you current directory where maybe a quota is in pla…
Comment: Error running pbrun fq2bam: No space left on device
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I know about this but why this is happening with 25 GB1000 genome project dataset not for 48 GB NCBI fastq dataset.
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Thanks for helping me.
I did get the Warp terminal ExpansionHunter command line to run and produce an output file.
But I believe the refe…
Comment: How to find the annotation file for GPL16956 platform of Arraystar human lncRNA
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You can find the probe sequences in this table: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?view=data&acc=GPL16956&id=25054&db=GeoDb_blo…
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please, Did you find any answer for this question as i am stuck in it now!!
Comment: Statistics for bins
by
GenoMax
152k
k127_5845587 2388
k127_1599072 5710
k127_4786624 15259
That is the name of the fasta header followed by length of…
Comment: Statistics for bins
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shevch2009
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It seems I have found a solution, but without an individual lengths of all scaffolds/contigs per bin....
seqkit stats -a -T /reassembled…
Comment: Statistics for bins
by
shevch2009
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The next code didn't provides what I need
seqkit fx2tab --length --name --header-line foo.fasta
I got strange table
k127_58455…
Comment: twist exome panel analysis
by
GenoMax
152k
With the exception of one sample looks like others have adequate coverage.
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