miRNA module not finding joined reads
Closed this issue · 2 comments
Hello, I am trying to use the miRNA module following prep, trim, and join (starting with SE reads) as
XICRA miRNA \
--input Prep/ \
--output_folder Prep/ \
--species eca \
--database miRBase \
--software optimir \
--single_end
everything up to this point worked as expected (NOTE - fastq-join
had to be installed separately and was not included following the conda-based installation). Upon executing the above code, I get the following error for each of the included test samples (n=2)
** ERROR: Only 1 fastq file is allowed please joined reads before...
When I run with --debug
I can see that the table being built are indeed pulling both R1/R2 instead of the trimmed and joined FASTQs which exist as expected in Prep/data/SAMPLE/join/SAMPLE_trim_joined.fastq
.
I'm sure I'm just missing something but please let me know if there are any other logs you would like to see.
Hi Jonah,
Thanks for pointing out about the fastq-join
missing dependency in the conda environment. I also found featureCounts
was missing in a completely fresh installation so be aware of that too. I have recently updated both the conda environment file and the python code, so you might find useful to re-install (at least the python code, make sure version >v.1.4.5 by typing pip install XICRA
)
Regarding the question you mentioned and the error you encountered using your data I suggest to remove some specs from you command: --output
and --single-end
I guess you should have generated a project folder containing the reads, qc results, and trimmed reads right? So you only require to use --input
flag as output results would be generated too there. Regarding the --single-end
flag, if you have already joined reads, you should not specify this flag anymore.
Your command would be
XICRA miRNA \
--input Prep/ \
--species eca \
--database miRBase \
--software optimir \
I have to say I haven't tested in any other species than human but it should work fine. Please let me know if it not works proprely.
Also, I prefer to use miraligner
than optimir
, although both are implemented. We found better performance using simulated reads in the XICRA paper (https://doi.org/10.1186/s12859-021-04128-1)
I have recently updated the code and I have added an example. Please run XICRA test
to get a set of reads to test the pipeline. Read the commands included in the test_subset.sh
generated and find the appropiate steps to reproduce the results.
Please, do not hesitate to contact me for further details.
Best regards,
Jose
Removing --single-end
worked, I must have misunderstood the help prompt. Thank you again!