SomaticSniper Posts

C: Converting a bunch or SRA files using fastq-dump split-files by genomax ♦ 48k
You can't have a space between `--split-files`. That was also a `1` (number one) not `l`(L) in th...
A: Converting a bunch or SRA files using fastq-dump split-files by jean.elbers • 170
1. You have `'` instead of ` 2. You need `$i` instead of `$f` 3. You need `--split-files` not ...
C: fastx_clipper problem in output by Sej Modha • 2.8k
It looks like you have not provided the adaptor string hence the program is looking for dummy def...
C: GO enrichment analysis using biomaRt by preetomregon • 0
ensembl_gene_id ensembl_transcript_id go_id name_1006 ...
C: Converting a bunch or SRA files using fastq-dump split-files by Mitra • 0
Thanks Genomax. Yes I do have space between -- and split-files in the loop. Also I tried with ls ...
C: I do not find DEG's with EdgeR that I do find with other tools by zoe • 0
With ballgown and noiseq I get between 250 and 400 DEG (depending on the upstream tools)
A: Bcftools view. FREQ inclusion error. by tcom111 • 0
[[Problem solved]] Dear all, Same as before, I switched to Float in accordance with finswimmer'...
C: data pre-processing for WGCNA Algorithm by modarzi • 0
Thanks, My data set is belong to TCGA. So, I found gencode.v22.annotation.gtf.gz as annotation f...
C: I do not find DEG's with EdgeR that I do find with other tools by genomax ♦ 48k
NOIseq and Ballgown are mentioned in orig post.
C: RAPIDR mask and build the reference by Kevin Blighe ♦ 19k
Your particular error is being thrown from line 112 of the R script: https://github.com/cran/RAPI...
C: Converting a bunch or SRA files using fastq-dump split-files by genomax ♦ 48k
Do you have a space between `-- ` and `split-files` in the loop? I would also use `ls -1` so only...
C: I do not find DEG's with EdgeR that I do find with other tools by geek_y ♦ 8.5k
If you have 2-3 replicates, its hard to judge the reproducibility. How many genes were DE betwee...

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