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Reference fasta file #25

Closed vetmohit89 closed 11 months ago

vetmohit89 commented 12 months ago

Dear,

I tested this tool with test data and it works absolutely fine. But I was not able to find these functions in IGV (2.15.2) File -> Load from File -> {sample_name}.bw for each sample Right click track. Select "Autoscale". Select "Maximum" under "Windowing Function".

Also, I am wondering which reference fasta (transcriptome or genome) I should use if I am just interested to know the differential expression of isomers? Can I use transcriptome reference file for this purpose?

Thank you Mohit

EricKutschera commented 12 months ago

I installed IGV 2.15.2 and was able to make the visualization from the example data. Here are screenshots: load_from_file

autoscale_maximum

You could also try https://github.com/Xinglab/rMATS-long which can make plots from ESPRESSO output

ESPRESSO requires the genome reference fasta

vetmohit89 commented 12 months ago

Thank you so much for reply. I am getting below warning message when running espresso_S.pl script:

samtools: /data/user/home/mbansal/.conda/envs/espresso/bin/../lib/libtinfow.so.6: no version information available (required by samtools) samtools: /data/user/home/mbansal/.conda/envs/espresso/bin/../lib/libncursesw.so.6: no version information available (required by samtools) samtools: /data/user/home/mbansal/.conda/envs/espresso/bin/../lib/libncursesw.so.6: no version information available (required by samtools)

Here was my sbatch file

!/bin/bash

SBATCH -J espresso.job

SBATCH -o espresso_1234%j.out

SBATCH -e espresso_1234P.%j.err

SBATCH -p pascalnodes-medium

SBATCH --time=48:00:00

SBATCH --mem=202400

SBATCH --ntasks=10

SBATCH --mail-type=ALL

module load Anaconda3/2022.05 module load SAMtools/1.12-GCC-10.2.0 conda activate espresso

perl ESPRESSO_S.pl \ -L samples.tsv \ -F GRCh38.p13.genome.fa \ -A /gencode.v43.annotation.gtf \ -O shGFP/

I used conda for intalling this tool and package has samtools. So I should not need to load samtools as module. It was giving error. I added samtools module load command and still getting this message.

Thank you Mohit

EricKutschera commented 11 months ago

Those warnings should be safe to ignore. I think it means that samtools didn't find the exact version of those libraries that it was expecting, but it was still able to use those libraries

I was able to install ESPRESSO to a conda environment today and use the samtools installed to that environment without seeing the warnings. You could try installing to a new conda environment to see if the warnings go away

vetmohit89 commented 11 months ago

Thank you so much Eric. I have only two replicates for each sample. I am wondering if I can still use rmats detect_differential_isoforms.py. Will it work with two samples per group?

Thank you Mohit

EricKutschera commented 11 months ago

I think you should be able to run https://github.com/Xinglab/rMATS-long/blob/main/scripts/detect_differential_isoforms.py if you have two sample groups each with 2 replicates. If you only have 1 replicate in each sample group then you may need to use the latest commit of rMATS-long instead of the v1.0.0 release