condition.csv and MAPPING_INFO.csv, and mixed PE and SR data in input fastq folder?

[Xiaofei-git]

Dear @hyunhwan-jeong ,

After running

SalmonTE.py quant --reference=hs --outpath=quant_out --exprtype=count example

, I am expecting get

clades.csv
condition.csv
CTRL_1
CTRL_2
EXPR.csv
MAPPING_INFO.csv
TARDBP_1
TARDBP_2

But, I missed MAPPING_INFO.csv and got phenotype.csv instead of condition.csv?

$ ls
CTRL_1      CTRL_2      EXPR.csv    TARDBP_1    TARDBP_2    clades.csv  phenotype.csv

Another question, could SalmonTE take mix PE and SR data in input folder (e.g. there are both single end and paired end fastq in example folder, is that OK for SalmonTE to get right outputs)?

Thanks a lot!

Best,

Xiaofei

[Xiaofei-git]

Hi @hyunhwan-jeong, I think it should work with mixture of SR and PE FASTQs. I tried to remove CTRL_1_R2.fastq in example folder and run SalmonTE.py count, and it went through. So, I believe it should work out.

But, I still can't get MAPPING_INFO.csv and condition.csv. Do you know the reason for this?

Thanks a lot!

Best,

Xiaofei

[Xiaofei-git]

Hi @hyunhwan-jeong, I think it should work with mixture of SR and PE FASTQs. I tried to remove CTRL_1_R2.fastq in example folder and run SalmonTE.py count, and it went through. So, I believe it should work out.

But, I still can't get MAPPING_INFO.csv and condition.csv. Do you know the reason for this?

Thanks a lot!

Best,

Xiaofei

@hyunhwan-jeong Could you help me to confirm if it can take the folder of mix SR and PE?

I think I made a mistake for the test of mix SR and PE. The run did not go through and I got as below:

SalmonTE.py quant --reference=hs --outpath=quant_out_test_mix --exprtype=count example_2
2021-09-23 05:08:34,748 Starting quantification mode
2021-09-23 05:08:34,748 Collecting FASTQ files...
2021-09-23 05:08:34,781 A paired-end sample and a single-end sample are placed together.