sharmi85

Please reply How to use Rat genome with circExplorer2? Its bit urgent

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...

i tried the reference gtf didn't work. When you had the same problem what did you do? On Mon, Dec 28, 2020 at 12:03 PM xczhang wrote: > Maybe you...

I tried a differnt file but doesnt work... Did you use th eknown genes file for the annotation? What command did you use to download the known genes txt file?...

Thank you so much This should help.. will try and update you back. Thanks Sharmi On Wed, Dec 30, 2020 at 6:32 AM xingma wrote: > I think the command...

Nope didn't work gave me the same error ###Start circRNA annotation Error: exonFrames field is being added, but I found a gene (ENSMUST00000221646.1) with CDS but no valid frames. This...

Thank you for your response. will update the version and try On Thu, Dec 31, 2020 at 2:13 PM xingma wrote: > Hi, this problem is caused by few transcript...

I have the following versions tophat2：tophat-2.0.12.Linux_x86_64 samtools：0.1.18.0 bowtie：1.0.0.0