Open rituparna-13 opened 2 years ago
Hi @phoenix1391
How many input FASTQ files are there? How long the reads are?
Hello Daniel, There are 194 fastq files as input and the read length is 100.
Hi Daniel, I am commenting here again since I did not hear back from you. Please let me know if you need more information.
Hi,
sorry but FusionCatcher does not support single end reads of 100bp long.
Cheers, Daniel
Hi Daniel,
I see. Thank you so much for letting me know.
Thanks, Ritu
Hi, I am running the FusionCatcher version 1.33 on single end RNA seq data with the following command:
../fusioncatcher/bin/fusioncatcher -d ../fusioncatcher/data/current/ --single-end --input ../from_Julia/ACGI428/FGC1222/ --output ./fusionCatcher_output/
It started unzipping the fastq.gz files and suddenly it starts looking for file init-0_FGC1222_s_3_AAGAGGCAAAGGAGTA.fastq which does not exists and it throws the following error:
I am not sure why is it trying to look for a file that does not exist or maybe I need to add some parameters to the command line for running it. Can you please help me solve this?