-
Hey guys,
I thought I would start of with this discussion already so people can think about it a bit. This sample sheet is not the one used for the sequencing run but specifically the nextflow work…
-
I'm trying to run GDCquery_Maf function
My code which i took from one of the tutorial
```
library(TCGAbiolinks)
library(maftools)
packageVersion("TCGAbiolinks")
[1] ‘2.22.4’
```
The e…
-
Dear,
I just checked the clone cluster effect on chromosome level. it look like below. I also tried different cluster methods mentioned in the function. but none of them could cluster all the simil…
yintz updated
9 months ago
-
I used the code "echo $(cat "HLA_reads.normal.fasta"|wc -l)/4|bc" to calculated the reads in your example fastq. but I only got the 125000 which is inconsistent with the parameters you provided "1665…
-
bash-4.2$ /data/CCRBioinfo/dalgleishjl/sv_mapping/svaba/bin/svaba run -t PAMHYN_Tumor.realigned.md.bam -n PAMHYN_Normal.realigned.md.bam -a PAMHYN_discovery_chr22 -k chr22 -G ucsc.hg19.fa -p 2
------…
-
Hello,
I wanted to ask something about cnvkit batch command.
```
cnvkit.py batch *Tumor.bam --normal *Normal.bam \
--targets my_baits.bed --annotate refFlat.txt \
--fasta hg19.fasta --…
-
**Describe the bug**
Cancer caller hangs in a reproducible manner. The caller is started with 24 threads. Slowly the number of active threads appears to dwindle as I can see the CPU usage go down. …
-
Our current workflow seems to assume that when there's a lesion mask, there's only one T1w image and only one mask. In [Neurostars #3776](https://neurostars.org/t/fmriprep-error-lesion-masks-over-sess…
-
Hi every one,
I installed the program Gap2Seq, and I found different bugs (or I hope) in the binary Gap2Seq.
when you ran the Gap2Seq like this:
Gap2Seq --vcf insertions_filtered.vcf -t 48 --re…
-
Hello,
Thank you for developing those fancy variant callers.
We conducted short-read RNA sequencing, and since we do not have a control sample, we are planning to call variants using the DeepSom…