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hyunhwan-jeong / SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
GNU General Public License v3.0
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running paired end data with SalmonTE #52

Closed amitpande74 closed 3 years ago

amitpande74 commented 3 years ago

Hi, I am trying to run the tool on paired end data.

./SalmonTE.py quant --reference=hs --outpath=outputPE --num_threads=8 PE1/ZI_JR_004_CTTGTA_L001_R1_001.fastq PE1/ZI_JR_004_CTTGTA_L001_R2_001.fastq 
2021-04-09 12:13:05,168 Starting quantification mode
2021-04-09 12:13:05,169 Collecting FASTQ files...
2021-04-09 12:13:05,170 The input dataset is considered as a paired-ends dataset.
2021-04-09 12:13:05,170 Collected 1 FASTQ files.
2021-04-09 12:13:05,170 Quantification has been finished.
2021-04-09 12:13:05,170 Running Salmon using Snakemake

Why is SalmonTE picking only 1 fastq file ?? Kindly help.

hyunhwan-jeong commented 3 years ago

Hi @amitpande74,

I suspect that the file name should be replaced with

PE1/ZI_JR_004_CTTGTA_L001_R1.fastq and PE1/ZI_JR_004_CTTGTA_L001_R2.fastq. Can you please try it?

Thank you,

Hyun-Hwan Jeong

amitpande74 commented 3 years ago

Dear @hyunhwan-jeong , After shortening the file names, it executes well. Thanks for your quick response.