TranscriptClean

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warning message: "Problem encountered while correcting transcript " single positional indexer is out-of-bounds

3

I have facing the follow error: /home/yanlab/Tools/TranscriptClean/TranscriptClean.py:449: UserWarning: Problem encountered while correcting transcript with ID 51ae56aa-43a8-4e20-bbc5-85ed8ea749bb. Will output original version. warnings.warn(("Problem encountered while correcting transcript " single positional indexer is...

criphg

invalid literal for int() with base 10: '1307=1' and UserWarning: Problem parsing transcript with ID 'transcript/10670'

3

Hi, I am getting issues like below when I run TranscriptClean "Correcting transcripts... invalid literal for int() with base 10: '1307=1' invalid literal for int() with base 10: '15=1' invalid...

philge

Hi, Thanks for an awesome piece of software. I have used TranscriptClean on large-scale assemblies with high success before. However I am now running a metatranscriptomics project in which I...

NiklasDreyer

Hi dear: I am having an issue with generate_report.R script.I attempt to run TC to correct my pacbio reads. Below are commands: python ~/TC/TranscriptClean.py --threads 30 --sam fruit.sorted.sam --genome final.genome.fasta...

gongjingtang

Is there a strong repair mode？

1

Hi: The software you have developed is excellent. I would like to know if there are any strong repair options including conventional SJ in the third generation including GTAG,GCAG. Or...

Trandamere

No such file or directory

4

Hi Dana I am having an issue with one particular file in my data set when I attempt to run it through TC. Below are commands python $TC --threads 6...

number-25

CIGAR operations out of range after splice junction correction

5

Hi, Since the update in #14 to update transcripts after correcting splice junctions, I get the following error. I think there may be a bug in the `rescueNoncanonicalJunction` function, which...

msto

Quality scores lost

2

I recently ran TranscriptClean on my PacBio reads, and it ran fine after making the changes you suggested (thanks!). However I noticed that the quality scores present in the input...

laurenfitch

Incompatible with CIGAR operators X/=

3

This tool fails for SAM files using X/= CIGAR operators instead of M, which are coming into more common use. It seems to be a quick fix to look for...

pdishuck

Hello, I've used transcriptclean before to clean up both Nanopore and PacBio Iso-Seq data and it has worked nicely on those long-read datasets, but recently, I tested it out on...

mbroad1