TALON

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tmp file

3

hi guys, In talon step, a talon_tmp dir was created. But many pybedtools.*.tmp files were generated in my root /tmp dir. How to fix it? Thx. Y

YZYwoazzzzz

Any chance of getting bam support?

4

Would there be any chance of getting Talon to accept bams as input? We have bams >100GB. We basically never store these as sams, since they'd be 0.5TB each. But...

oneillkza

ValueError: No reads detected. Make sure your dataset names are correct.

10

Hello! I'm testing out TALON on some Nanopore sequencing reads. After setting up the database and specifying the config file TALON's `get_read_annotations.py` would run and throw this exception: `ValueError: No...

chalybes

Roll config file into command line parameters?

1

Right now half of the parameters to Talon are passed directly (e.g. `--db`, `--build`), but the other half (sample info, sam file) are passed via a separate comma-separated file. This...

oneillkza

Failed to open file talon_tmp/interval_files/1_10554_248944156.bam

2

Hello Talon Team, I got an error while running the talon annotate step. Could you please help me with this? Version: v5.0 Command used: talon --f config_file.txt --db talon_gencode_v37_gtf.db --build...

sid-sethi

Transcripts identified possibly without supporting reads.

7

Dear TALON team, We are analysing a nanopore human dataset using TALON and came across some interesting transcripts with a high abundance. Looking further into these transcripts, we hoped to...

JasperBoom

ValueError: Annotation name 'transcriptome' not found in this database. Try one of the following:

1

Hello TALON group, After running your program I get this message: **ValueError: Annotation name 'transcriptome' not found in this database. Try one of the following:** 'transcriptome' is the name that...

simonemoro

Export fasta from TALON database?

1

Hi, thanks for the excellent software! This is a feature request, or if there is a way to do this already, I'd like to know how. I want to export...

joelnitta

Hello, Seems that TALON's logic fails with python installations >= 3.8. When running on the test data provided with your distribution with the commands provided the program fails with the...

NatPRoach

The fix would be to pass the same pyfaidx genome object to each of the threads instead of initializing a new one on each different thread. Pyfaidx creates and accesses...

fairliereese