CLEAR
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YangLab
direct comparison of circular and linear RNA expression
So I'm trying to run clear_quant on a RNA-seq file I obtained online (Ribo-), but I cannot seem to move past the following error: > ###Parameters: > Namespace(bowtie1='/home/nilu/Alignment_db/base_files/ensembl/bowtie/bowtie_index', genome='/home/nilu/Alignment_db/base_files/ensembl/base_files/Homo_sapiens.GRCh38.dna.primary_assembly.fa', gtf='/home/nilu/Alignment_db/base_files/ensembl/base_files/Homo_sapiens.GRCh38.109.gtf',...
Hi, Thanks for CLEAR. I am in troubles using CLEAR and looking for solutions. I need your help and this is the error log. ```bash ###Parameters: Namespace(bowtie1='/home/ionadmin/likun/13SequencingData/00.ref/GRCh38_bowtie_index/GCA_000001405.15_GRCh38_no_alt_analysis_set', genome='/home/ionadmin/likun/13SequencingData/00.ref/02.circ/hg38.fa', gtf='/home/ionadmin/likun/13SequencingData/00.ref/gencode.v39.annotation.gff3', hisat='/home/ionadmin/likun/13SequencingData/00.ref/grch38_snp_tran/genome_snp_tran',...
Greetings, I tried to use the CLEAR pipeline under a python3 environment, and it worked well until the TopHat, where I got: `TopHat2 is not compable to python3. You can...
Hi, In the mapping with tophat-fusion step, I get the below error: ``` $ clear_quant -1 206_1.fq.gz -2 206_2.fq.gz -g /library/hg19.fa -i /library/hg19.fa -j /library/hg19.fa -G /library/hg19.genes.gtf -o 206 -p...
I run the software with the following parameters： `clear_quant -1 ~/biodata/hcc-ribo/rmrRNA/LC501_tumor_totalRNA.derrRNA.fq.gz -g ~/biodata/index/GRCh38/GRCh38.primary_assembly.genome.fa -i ~/biodata/index/GRCh38/GRCh38 -j ~/biodata/index/GRCh38/GRCh38 -G ~/biodata/annotation/gencode.v35.annotation.sorted.gtf -o ~/tools/CLEAR-master/test2 -p 18` No error was reported during the process,...
hello! First thanks a lot for providing a fantanstic tool for circRNA analysis! I have an issue when running circ_quant, the nohup.out file says that: **TypeError: 'NoneType' object is not...
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...
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...
Hi, I have two sets of sequencing data for the same cell lines: 1. Total RNA-Seq (ribo-) 2. circRNA-Seq (ribo- and RNaseR+) Referring to the [CLEAR article](https://doi.org/10.1016/j.gpb.2019.11.004), it says: >...
Hi, Is this version available in anaconda yet? Are you planning to add it soon? Thanks.