novartis / eqp-cluster Goto Github PK

Hi there,
Many thanks for releasing this code to the community. Regarding the statement "due to the way the custom junction Fasta file is created EQP-cluster works best with reads of length 101bp or less" is there a way to improve the pipeline to work well with longer reads? We have quite often 150bp reads that we'd like to use

Hi,

I successfully build the bowtie2 index and I try to run analysis using your sample in samples.tgz. However, I encounter this error.

sh bin/process-samples.sh split

bin/process-samples.sh: 546: bin/process-samples.sh: source: not found
bin/process-samples.sh: 640: bin/process-samples.sh: [[: not found
bin/process-samples.sh: 647: bin/process-samples.sh: [[: not found
bin/process-samples.sh: 653: bin/process-samples.sh: [[: not found
bin/process-samples.sh: 780: bin/process-samples.sh: [[: not found
bin/process-samples.sh: 1107: bin/process-samples.sh: [[: not found
Samples:

I tried to set up $PROG_DIR to the location where setup.sh is located. However, I still get the same error message.
I try both just unpacked samples.tgz and samples that contain only two fastq.gz files.

Is there any recommendation that I should try?

Thank you,
Chai

Hi,

I tried to install EQP-cluster and I run into the dependency issue. I have bowtie2 2.2.3 and your program require >=2.0.5; however, the installation still exit. Do you have any recommendation?

Thank you,
Chai

sh create-bowtie2-indices.sh
Extracting directory exon-pipeline-files
create-bowtie2-indices.sh: 287: create-bowtie2-indices.sh: source: not found
Please use bowtie2-build version >= 2.0.5. Found version: 2.2.3 ... exiting

Hi,

When I try to analyze exon counts generated by EQP with DESeq2 package I get an error:

"Error in DESeqDataSet(se, design = design, ignoreRank) :
some values in assay are not integers"

And when I go and check the results, indeed there are some decimal number. Why EQP produces counts that are decimal numbers and how I can fix this problem ?

Thanks.

Hello,

I installed the EQP-cluster as per the instructions & it seems to have installed without any problems (creation of Bowtie2 indices completed).

When I attempt to use Split though (./process-samples.sh split), I get the message below:

Samples: sample1 sample2
Sample sample1
Split job SP-sample1-209 is still in job queue ... skipping sample sample1
Sample sample2
Split job SP-sample2-209 is still in job queue ... skipping sample sample2

This also happens when I try the -noqsub 1 option. I also tried using my own data but the same message appears.
There is also no data in the log and fastq files subdirectories in the sample 1, 2 directories.

Wasn't able to find anything online about this.
I was wondering what I should try?
Please let me know if there is something I can clarify

Thanks in advance!
Hunter