jaredslosberg / get_sra_fastqs Goto Github PK
View Code? Open in Web Editor NEWSnakemake workflow to grab raw fastqs from SRA from SRR, SRX, SRP, or PJRNA accession numbers
Snakemake workflow to grab raw fastqs from SRA from SRR, SRX, SRP, or PJRNA accession numbers
In addition to raw fastqs, also grab metadata for an experiment which would include things like tissue, prep, experiment/run, paired/single end... Either do this with XML parsing or find a package that already does it
using perl xpath to strip metadata from xml files crashes for SRA projects with many samples (eg SRP056477)
error message:
Ran out of memory for input buffer at /home/[...]/lib/site_perl/5.26.2/x86_64-linux-thread-multi/XML/Parser/Expat.pm line 474.
free(): invalid next size (normal)
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