I am converting the fq.gz. files (which are the results of the mgi study) to bam files to view on igv.

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Hey everyone, before i start apologies for the inconvenience cause of my wrong or inappropriate use of terms. I take some fails of bwa mem lately. As i mentioned in the post title i'm working with fastq files. And i get:

[E::main_mem] fail to open file '/mnt/MGI-R4/L01/(sample_name)_(barcode_number)_1.fq.gz'. 

and

[main_samview] fail to read the header from "-".

And here is my command:

bwa mem -M -t 8 ~/genome/hg19.fa /mnt/MGI-R4/L01/(samplename)_(lane)_(barcodenumber)_1.fq.gz /mnt/MGI-R4/L01/(samplename)_(barcodenumber)_2.fq.gz | samtools view -o (samplename)_(lane)_(barcodenumber).bam -

i know that my command works because i used to convert. Can you please help me?


mem


samtools


bwa

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