RNA-seq Pipeline for Known Transcripts: Difference between revisions
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==Sequence Quality and Trimming== | ==Sequence Quality and Trimming== | ||
# Run FASTQC to assess quality of reads from sequencer and: | # Run FASTQC to assess quality of reads from sequencer and: | ||
# FASTQC available at http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ | |||
## Open run_fastqc on a windows machine. Individually open each sequence file and allow it to analyse. Save this report. | |||
## Check this report to decide if sequences need to be trimmed or discarded. | |||
===Filter Sequences Using FastX-Toolkit=== | |||
# Filter for quality, if applicable | # Filter for quality, if applicable | ||
# Trim, if applicable | # Trim, if applicable | ||
==Generate a Reference Genome== | ==Generate a Reference Genome== | ||