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hemberg-lab / MicroExonator

Snakemake pipeline for microexon discovery and quantification
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example of local_samples.tsv #46

Open CharlotteAnne opened 8 months ago

CharlotteAnne commented 8 months ago

I can't find an example of local_samples.tsv?

geparada commented 8 months ago

Hi Charlotte,

Please check Examples/Runs/COSMIC/local_samples.tsv. There you can find an example of how this file should look like.

https://github.com/hemberg-lab/MicroExonator/blob/master/Examples/Runs/COSMIC/local_samples.tsv

zyh4482 commented 6 months ago

May I ask what if it is a pair-end fastq? Would you mind providing an example for this case? Because my data are huge and collected from various sources, it is not possible to use the implemented config.py to prepare all the data. Any suggestion would be grateful! Another question is: what should be the directory to put the local_samples.tsv file in?

tebioinformatics commented 2 months ago

Could you please advise on how to handle pair-end FASTQ files? I would greatly appreciate it if you could provide an example for this case. Given that my data are vast and collected from various sources, it is not feasible for me to use the implemented config.py to prepare all the data. Any suggestions you might have would be greatly appreciated.

local_samples_example.txt We have created the local_samples.tsv file in the format as shown in the attached document. Could you please confirm if the format is correct?