sharmi85

want to use circexplorere2 for rat genome (Rnor_6.0)

1

Hello I want to use circExplorer2 for the rat (Rattus novergicus) dataset. I was trying to fetch the rat genome using the command: fetch_ucsc.py Rnor_6.0 fa Rn6.fa it's giving me...

tophat fusion error

2

I have installed all the bowtie, tophat and samtool packages recommended for the tophatfusion run, but getting this error, it cant locate my samtools. I have version you have asked...

exonFrames field is being added, -genePredExt but no valid frames

6

Hello. I am trying to use CLEAR for my data set and running the following command: clear_quant -1 /userdata/sharmishtha/Hela/trimmedFastqFiles/trim_HeLa-AMT-1_R1.fastq.gz -2 /userdata/sharmishtha/Hela/trimmedFastqFiles/trim_HeLa-AMT-1_R2.fastq.gz -g /userdata/sharmishtha/ref_and_anno/hg38/hg38.fa -i /userdata/sharmishtha/IndexFiles/hg38/hisat2index/hg38_hisat2_index -j /userdata/sharmishtha/IndexFiles/hg38/bowtie1_index/bowtie1_index -G /userdata/sharmishtha/IndexFiles/hg38/hg38_kg.gtf -o...