Changes from v0.43.1
kallisto can now project pseudoalignments from transcripts down to genomic coordinates. This requires a GTF file corresponding to the transcriptome used to construct the index. The resulting BAM file is sorted by genomic coordinates and indexed.
--pseudobamoption works as before in transcript coordinates, but creates a single output
pseudoalignments.bamin the output folder. This mode no longer writes SAM format to standard output, but writes the binary BAM file directly. Multithreaded
--genomebamoption writes pseudoalignments to the file
pseudoalignments.bamin sorted genomic coordinates, requires a
--gtfoption and optionally a
--single-overhang option that does not discard reads where unobserved rest of fragment is predicted to lie outside a transcript. This is mainly useful for mapping 3’ biased reads from single cell experiments.
Adds QC information to
run_info.json in the output folder
The added fields are
n_pseudoaligned: number of fragments that could be pseudoaligned
p_pseudoaligned: percentage of fragments that could be pseudoaligned
n_unique: number of fragments that could be pseudoaligned to a unique target sequence
p_unique: percentage of fragments that could be pseudoaligned to a unique target sequence