Changes from v0.43.1

BAM!

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.

• --pseudobam option works as before in transcript coordinates, but creates a single output pseudoalignments.bam in the output folder. This mode no longer writes SAM format to standard output, but writes the binary BAM file directly. Multithreaded --pseudobam works now
• --genomebam option writes pseudoalignments to the file pseudoalignments.bam in sorted genomic coordinates, requires a --gtf option and optionally a --chromosomes options set.

quant mode

Adds 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.

JSON output

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