RSeQC

[yyoshiaki]

http://rseqc.sourceforge.net/ http://kazumaxneo.hatenablog.com/entry/2018/02/27/235531

multiqcでも表示できそう https://multiqc.info/docs/ Supported scripts:

• bam_stat
• gene_body_coverage
• infer_experiment
• inner_distance
• junction_annotation
• junction_saturation
• read_distribution
• read_duplication
• read_gc

[yyoshiaki]

bamが必要だが。。。

https://salmon.readthedocs.io/en/latest/salmon.html

Genomic vs. Transcriptomic alignments

Salmon expects that the alignment files provided are with respect to the transcripts given in the corresponding fasta file. That is, Salmon expects that the reads have been aligned directly to the transcriptome (like RSEM, eXpress, etc.) rather than to the genome (as does, e.g. Cufflinks). If you have reads that have already been aligned to the genome, there are currently 3 options for converting them for use with Salmon. First, you could convert the SAM/BAM file to a FAST{A/Q} file and then use the lightweight-alignment-based mode of Salmon described below. Second, given the converted FASTA{A/Q} file, you could re-align these converted reads directly to the transcripts with your favorite aligner and run Salmon in alignment-based mode as described above. Third, you could use a tool like sam-xlate to try and convert the genome-coordinate BAM files directly into transcript coordinates. This avoids the necessity of having to re-map the reads. However, we have very limited experience with this tool so far.