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Hi
ctat_mutations.v3.0.0.simg used with GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play is giving the EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParamet…
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hi there:
I got a erorr when I ran the script `build_ctat_lib.sh`, the error message is following:
* Running CMD: hmmscan --cpu 4 --domtblout PFAM.domtblout.dat ./source_download/PFAM.domtblou…
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Hello there,
I am trying to run the rnaseq_mutation_pipeline.py using the instructions provided in the Readme.txt. However, I keep getting an error regarding my input .fa files. Could you provide an e…
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I was running the ctat-mutation pipeline with singularity.
I have done the "test" data before
Here is my script:
singularity exec -e -B ${CTAT_GENOME_LIB}:/data/hemberg/jaewon/ctat/new5/GRCh37_ge…
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I saw GRCh37 v19 CTAT source_lib in https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/, but I have finished STAR with GRCh37 v27 refrence and got the junction file. Is it necessary to build a …
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Hello!
I'm building a ctat_genome_library in preparation to run STAR-Fusion, but I came across an error when I ran "prep_genome_lib.pl". It ran into an issue when trying to run "index_pfam_domain_…
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Hi, Brian, I am running the CTAT-mutations (v3.2.0) pipeline, the library version is StarFv1.10. I used the commamd:
$ nohup time ~/src/CTAT-Mutations-v3.2.0/ctat_mutations --cpu 15
--genome_lib_d…
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Hi,
after following https://github.com/NCIP/ctat-mutations/wiki/CTAT-mutations-installation,
by using docker i run RNA-seq data.
but it occurs error printing
> unrecognized parameter name…
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Hi,
I am trying to run a test with a cell line with a know mutation:
PC9 (NSCLC) cells with EGFR deletion
https://mupit.icm.jhu.edu/MuPIT_Interactive?gm=chr7:55205393
First, I ran the same a…
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Hi,
Thanks for developing `wgatools`, it looks very promising.
I am particularly interested in visualizing some `.maf` files that I generated by progressive alignment with `cactus`, and then c…