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Specifically, when strand information is coded as "?". Right now, these junctions are dropped. It would be good to instead offer the option of converting the "?" to the un-stranded character "*", sinc…
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Running in `/dcs04/lieber/lieber_jhshin/RNAseq_LIBD4020/spqz/p2_n443` - see the SPEAQeasy.log there.
I tried resuming this a few times but I couldn't figure out why I keep getting this error in this…
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Just had a run of SPEAQeasy (locally) on a 30-sample dataset where the compressed raw data (fastq.gz) are about 175 GB total.
Running that on a fast SSD with about 1.8 TB available storage, the SSD …
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Currently, `scripts/generate_logs.sh` makes the assumption that all nextflow processes have completed (whether successfully or not). However, whenever the pipeline halts before completing (e.g. due to…
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There are situations where users want to change e.g. featureCounts options, or bring in already prepared read alignments (sorted BAMs) so in such cases it would benefit to have the option to skip the …
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check if the column is present (since not all experiments have this) but if its present, include in the merging
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Now that there are multiple versions of the RNAscope data, from different settings on HALO, a more automatic way to build then summarize `HALO_all` would be useful. Building of this script [01_explore…
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Hello,
I am having the next error:
Error executing process > 'BuildAnnotationObjects'
```
Caused by:
Process `BuildAnnotationObjects` terminated with an error exit status (1)
Command…
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# General Notes
This repository serves as a mostly automa…