Open kicheolkim opened 4 years ago
Hi, Thanks for the feedback, I think this line is telling something interesting:
04/16/2020 09:17:37 INFO-mirtop.libs.logger(143): Reads without precursor information: 11124
Can you send the command used?
As well, can you check whether the miRNA in the sRNAbench matches the names in the GFF from miRBase you are using?
Just to be sure that is not a bug in master:
Can you try the devel version of mirtop?
Thanks!
Thank you for the quick reply!! I've run with develop version but it's still empty.
I used fasta and gff3 files downloaded from the miRBase website, so, I believe they match. And it works well with output from a different mode. (add: confirmed name match between hsa.gff3 and hairpin.fa)
I used command as below:
mirtop gff --sps hsa --hairpin /Users/kicheol/working/pipeline_dev/smallRNA/Test_Qiaseq/output/test_v2.2_isomiR/hairpin.fa --gtf /Users/kicheol/working/pipeline_dev/smallRNA/Test_Qiaseq/output/test_v2.2_isomiR/hsa.gff3 --format srnabench --out-format gff -o ./ ./S400001603 ./S400001616 ./S400001617
And here is the log file with '-d' option in case it's helpful for you.
Hi, thank you for the log file, for some reason the files has Chr information there as well. So mirtop is seeing this line:
mature#hsa-miR-92a-3p#sense#chrX;hsa-mir-92a-2,48,70
and it is extracting the precursor as: chrX;hsa-mir-92a-2
I guess sRNAbench is was run with some other flag, can you pass me you command line used on that step?
Thanks!
I used this command:
java -jar $sRNApath/sRNAbench.jar input=$inputDir/$fileName output=$outputDir/"$sample" p=$thread dbPath=$dbPath adapter=$adapter minReadLength=15 holdNonAdapter=true umi=3pA12 qualityType=mean minQ=20 microRNA=hsa mature=mature.fa hairpin=hairpin.fa species=hg38 alignType=n seed=18 noMM=1 predict=false isoMiR=$isomir
sRNAbench has two modes: library mapping and genome mapping. I used genome mapping mode in this output, I think that's why it has a chromosome tag. It works well with output from library mode.
Thanks!!
Expected behavior and actual behavior.
I tried input using output from sRNAbench genome mapping mode. I expected gff output with miRNA/isomiR information and counts, but the file was empty like this:
Here is the log file:
Steps to reproduce the problem.
It's working with the output from library mapping mode of sRNAbench with same sample. I saw the contents in gff output. But the gff was empty only when I used genome map mode output.
Specifications like the version of the project, operating system, or hardware.
I'm using mirtop 0.4.23, and sRNAbench version is 2.0 - 4/2020
Thanks!!