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5 votes
Accepted

Using variables with fasterq-dump?

You have an obvious error in your shell script that should have given you an error message: sra_code = "DRR163""$i" Should be: ...
terdon's user avatar
  • 10.2k
2 votes

How to split FASTQ reads without re-running `fastq-dump`?

As reads have equal length, so all 152-bp reads can be split into 76-bp read pairs accordingly. We can get Read1 by trimming the tail 76 bp, and get Read2 by trimming the heading 76 bp. No need to re-...
Zhuqiang Zhang's user avatar
2 votes
Accepted

How to split FASTQ reads without re-running `fastq-dump`?

My comment above mentions the slow IO for the Python code (it was iterating at ~ 3600 reads/s, which, for a FASTQ with 500M reads would take ~1.6 d to complete), so I tried an alternative method that ...
James Hawley's user avatar
  • 1,384
2 votes
Accepted

Error output in nextflow pipeline using fasterq-dump

Each nextflow process looks in its working directory for the files listed in output: . In your script: you already direct the ...
Pallie's user avatar
  • 706
1 vote
Accepted

Downloading multiple SRA files as FASTQ files using SRA Toolkit

That is a classical problem where the folder containing the binary of the tool is not in PATH, see for example https://askubuntu.com/questions/109381/how-to-add-path-of-a-program-to-path-environment-...
ATpoint's user avatar
  • 1,326

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