combining_featCount_tables.py demonstration

by rnnh 5 years ago

GNU/Linux • xterm-256color • bash 2447 views

This is a video demonstartion of combining_featCount_tables.py.

In this video, combining_featCount_tables.py is used to combine the following featureCounts tables:

feature_counts_SRR8933506_S_cere_GCF_000146045.2_R64_genomic.fna.tsv
feature_counts_SRR8933509_S_cere_GCF_000146045.2_R64_genomic.fna.tsv
feature_counts_SRR8933510_S_cere_GCF_000146045.2_R64_genomic.fna.tsv
feature_counts_SRR8933511_S_cere_GCF_000146045.2_R64_genomic.fna.tsv
feature_counts_SRR8933512_S_cere_GCF_000146045.2_R64_genomic.fna.tsv
feature_counts_SRR8933530_S_cere_GCF_000146045.2_R64_genomic.fna.tsv
feature_counts_SRR8933531_S_cere_GCF_000146045.2_R64_genomic.fna.tsv
feature_counts_SRR8933532_S_cere_GCF_000146045.2_R64_genomic.fna.tsv
feature_counts_SRR8933533_S_cere_GCF_000146045.2_R64_genomic.fna.tsv
feature_counts_SRR8933534_S_cere_GCF_000146045.2_R64_genomic.fna.tsv
feature_counts_SRR8933535_S_cere_GCF_000146045.2_R64_genomic.fna.tsv
feature_counts_SRR8933536_S_cere_GCF_000146045.2_R64_genomic.fna.tsv
feature_counts_SRR8933537_S_cere_GCF_000146045.2_R64_genomic.fna.tsv
feature_counts_SRR8933538_S_cere_GCF_000146045.2_R64_genomic.fna.tsv
feature_counts_SRR8933539_S_cere_GCF_000146045.2_R64_genomic.fna.tsv

These featureCounts results were generated using the following fastq-dump_to_featureCounts.sh command:

$ bash ../scripts/fastq-dump_to_featureCounts.sh -a S_cere_GCF_000146045.2_R64_genomic.gtf -f S_cere_GCF_000146045.2_R64_genomic.fna --verbose -p 3 SRR8933506 SRR8933509 SRR8933510 SRR8933511 SRR8933512 SRR8933530 SRR8933531 SRR8933532 SRR8933533 SRR8933534 SRR8933535 SRR8933536 SRR8933537 SRR8933538 SRR8933539

In this command, the full genome sequence (S_cere_GCF_000146045.2_R64_genomic.fna) and genome annotation (S_cere_GCF_000146045.2_R64_genomic.gtf) for Saccharomyces cerevisiae S288C are used.

These featureCounts results were then combined using the following command:

$ python ../scripts/combining_featCount_tables.py

Running this script combines all the featureCounts results in a directory into a single CSV file. If a custom name for this file is not given, it will be given a name using this scheme: featCounts_{species}_{date}.csv.

Version of the script used in this video: https://github.com/rnnh/bioinfo-notebook/blob/a2e4e91507187ae48f6e4bbbad3c700afb68d2a3/scripts/combining_featCount_tables.py

Made for https://rnnh.github.io/bioinfo-notebook/

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