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wyang17 / SQuIRE

Software for Quantifying Interspersed Repeat Expression
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Not picking fastq files #62

Open GiwaAO opened 3 years ago

GiwaAO commented 3 years ago

I am running squire Map step for paired end data. However, when i list the files for each read (read 1 and 2), it doesn't work properly. It seems not to be picking up the files, and only picks one (the last one on the list). What could be wrong? I separated the fastq files with comma (,) as directed.

GiwaAO commented 3 years ago

Also, What is the appropriate name for the -n argument in squire Count. I ran squire Count -m folder -r 150 -n .bam -b 'mm10' -p 15 -s 1 -v, and got a successful result. However the sample columns in the result files were populated by .bam and not the sample names. This created a problem as squire Call gave an index out of range error.

My sample files are titled thus; SRR00001_1.fastq.bam, SRR00002_1.fastq.bam, SRR00002_1.fastq.bam etc. What should the -n argument be?

fernandogs97 commented 3 years ago

Hello GiwaAO, First make sure that when you start with the map step you don't introduce any space between the comma (,) and the path to the second read (If this is not your error, could you please put the code here?) In the other hand, the -n argument purpose is for giving to the output a complete name. If your sample name is SRR00001_1.fastq the -n argument should be -n SRR00001_1.

GiwaAO commented 3 years ago

Okay. Will try these out. Thanks