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* Document the association of total genes and transcripts by tool
- [ ] star count
- [ ] htseq
- [ ] feature count
- [ ] salmon
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Error raised during the processing of BAM input. This occurs for only some of the bam files, not all, which went through identical processing pipeline. This affected downstream package which depends o…
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After installing quant3p, the test run with the example data fails with an error, for the output see below. As far as I get it, it is missing pybedtools. However, I have installed version 0.8.1 as co…
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I'm attempting to create a reference for T2T (HS1). Ran into two issues:
## Problem 1
Running `renee build` and had the rule `qualimapinfo` fail. The `.err`. and `.out` log were unhelpful. The scr…
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query
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Major blocker for this is dependence on HTSeq, which is python2 only and unlikely to be upgraded
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- [x] Star-Stringtie-DESeq2
- [x] Star-Stringtie-EdgeR
- [x] Star-Stringtie-Ballgown
- [x] Star-Cufflinks-Cuffdiff
- [x] Star-Cufflinks-Ballgown
- [x] Star-HTSeq-DEXSeq
- [x] Star-Featurecounts-…
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```
What steps will reproduce the problem?
1. runing star with parameters:
star --genomeDir $GENOME_DIR \
--readFilesIn $READS1 $READS2 \
--runThreadN $TREADS \
--genomeLoad LoadAndKeep \
--alignInt…
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MBP:merged Staj$ mefit -s casper -r1 69_S69_L001_R1_001.fastq -r2 69_S69_L001_R2_001.fastq -p casper.params2 -nonovlp -n 15 -avgq 20
Traceback (most recent call last):
File "/Users/Staj/tools/bin/me…
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Dear Collegue,
I wrote the follow code but I get this error from the TCGAanalyze_Preprocessing function:
Error in `$