TranscriptClean

TranscriptClean copied to clipboard

Hi I generated splice junction from short reads from the same samples using the followinghttps://github.com/mortazavilab/TranscriptClean/wiki/TranscriptClean-Tutorial#noncanonical-splice-junction-correction ``` STAR --runThreadN 64 \ --genomeDir "$genomeDir" \ --readFilesCommand zcat \ --readFilesIn "../${sample_prefix}__SR/fastq_SR/${sample}_SR_1.fq.gz" "../${sample_prefix}__SR/fastq_SR/${sample}_SR_2.fq.gz" \...

MustafaElshani

Running with 12 threads following basic usage example in README.md ``` Traceback (most recent call last): File "/rsrch5/home/epi/bhattacharya_lab/software/longreadapps/TranscriptClean_venv/bin/transcriptclean", line 33, in sys.exit(load_entry_point('TranscriptClean', 'console_scripts', 'transcriptclean')()) File "/rsrch5/home/epi/bhattacharya_lab/software/longreadapps/TranscriptClean_venv/TranscriptClean-master/TranscriptClean/TranscriptClean.py", line 37, in main...

sbresnahan

Hello and thank you for developing TranscriptClean!!! I have a small issue/observation after running the basic command line for my dataset (ONT cDNA, aligned with minimap2). Here is my bash...

AlexFryd

Significant Read Reduction in Specific Samples After Running TranscriptClean

1

Hi, I encountered a problem while processing data with TranscriptClean. Specifically, a significant reduction in read count was observed in a subset of samples, while others remained unaffected: Affected samples:...

tabatakenshiro