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FASTQ is a file format use to store short reads and their quality values

0 votes
1 answer
75 views

Nvidia Parabrick fq2bam pipeline error - No such file or directory

I am trying to implement Nvidia-parabrick fq2bam pipeline to process my WES dataset. The reason for opting this pipeline is the huge number of samples (1004) which take many months to process for soma …
1 vote
Accepted

Nvidia Parabrick fq2bam pipeline error - No such file or directory

My query was answered by NVIDIA Parabrick developer team. The installation instruction are available at https://forums.developer.nvidia.com/uploads/short-url/t5uXsZgdMXx0G2wDcYamFl9sO2x.pdf.
2 votes
2 answers
420 views

Filter reads belonging to unique sequences with threshold

I have CLL samples as fastq files and I want to remove those reads which have a unique sequence with less than 10 read counts each. … I think it's OK to stick with bash/awk for fast fastq file processing. What am I missing here, or is this command wrong. Can anyone suggest me the right and fast way to do it?? …
3 votes
1 answer
257 views

Fast processing of fastq data

I am trying to write python script for customized filtering for fastq file (size >3 GB). … I need suggestions to improve this script to make fastq file processing faster. …
9 votes
1 answer
656 views

Why does this human bam file only have one copy of each chromosome?

But in either fastq file or bam file in WES data, I always find only one copy of each chromosome. Q1: Where is the other gene copy in the sequence or have I have missed something? …