-
Dear Collegue,
I wrote the follow code but I get this error from the TCGAanalyze_Preprocessing function:
Error in `$
-
Via email from MKM try the following changes:
1. Use htseq-count parameters `htseq-count --format=bam --stranded=reverse -r 'pos' --mode=intersection-nonempty $IN_FOLDER/$FILE/merged.bam $GTF > $OUT_F…
-
Hi,
I wanted to run below query via GDCquey:
`query
-
gdcParseMetadata error
```R
> metaMatrix.RNA
-
```
What steps will reproduce the problem?
1. runing star with parameters:
star --genomeDir $GENOME_DIR \
--readFilesIn $READS1 $READS2 \
--runThreadN $TREADS \
--genomeLoad LoadAndKeep \
--alignInt…
-
An output format that contains counts for all transcripts (in standard order) would be useful for downstream analysis. Like most other quant software (htseq-count, kallisto, salmon)
-
Build failing for dexseq/v3.9
```
E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?
The command '/bin/sh -c echo 'deb http://mirror.math.princeton.edu/pub/ubun…
-
Hi
I have a general question pertaining to quantifying QuantSeq data and comparing Salmon vs the alignment methods recommended by Lexogen (Star/Bowtie followed by htseq to get read counts per gene)…
-
**Question**
We are comparing different aligners and quantifiers to see their impacts on the same RNA-Seq raw data. Of course, it took long time to run one run. My guess is that we do not have to r…
-
The code is here:
readsToWiggle.pyx
read_start = read.positions[0]
read_stop = read.positions[-1]
This will only work for positive strands, negative strands will get the END of the read. Fix is eas…