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Posts by simo.aufiero
... Hi Spin, this is the command line that I used to perfom the analysis: python mapsplice.py -p 16 --bam -o mapsplice_out001 -c Chromosomes -x BowtieIndex/genome -1 paired-001.R1.fastq -2 paired-001.R2.fastq --gene-gtf gencode.vM16.annotation.gtf --fusion-non-canonical --filtering 1 --min-map-len 25 - ...
... Hi Guanghao Li, I had the same problem. I am running mapsplice using the genome reference mm10. I did the analysis in the past by using mm9 and mapsplice pipeline finished without any problem with that genome reference. What genome reference are you using? Simona ...
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