Comments (1)
It may be related to compatibility of different tools. bowtie (v0.12.9), tophat2 (v2.0.12) and hisat2 (v2.0.5) works well. You may try these versions.
from clear.
Related Issues (20)
- Installation issue HOT 1
- Tophat-fusion error HOT 7
- CLEAR with STAR alignment HOT 1
- Feature Request: Calculate FPBlinear for all genes HOT 1
- exonFrames field is being added, -genePredExt but no valid frames HOT 6
- single end reads HOT 2
- CodingErrorFound HOT 1
- tophat fusion error HOT 2
- ValueError: too many values to unpack HOT 1
- TypeError when Running CLEAR: 'NoneType' object is not iterable HOT 1
- NO quant or circular output HOT 2
- Issue when using clear_quant HOT 2
- IOError: [Errno 2] No such file or directory: circ/genePred.tmp HOT 1
- CLEAR: python2 or python3? HOT 3
- STAR bam files? HOT 1
- Tophat2, Bowtie, Samtools compatibility problems HOT 1
- CLEAR availability in anaconda
- FPBcirc vs FPBlinear comparison from different sequencing data
- Hisat2 runs extremely slow HOT 1
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from clear.