sequences dropped from the index

[fklirono]

Hello,

kallisto (0.44.0) seems to be silently dropping sequences from the index.

Working example:

• download circBase hg19 circRNA sequences.
• count them (140790)
• index them and count again how many targets are included in the index (92509)

Is there a reason why some sequences are not indexed?

Code to reproduce example:

wget 'http://www.circbase.org/download/human_hg19_circRNAs_putative_spliced_sequence.fa.gz' | gzip -d -c > human_hg19_circRNAs_putative_spliced_sequence.fa

sed -n '/^>/p' human_hg19_circRNAs_putative_spliced_sequence.fa |  wc -l 

kallisto index -i human_hg19_circRNAs_putative_spliced_sequence.fa.fai human_hg19_circRNAs_putative_spliced_sequence.fa

kallisto inspect human_hg19_circRNAs_putative_spliced_sequence.fa.fai

[fklirono]

sorry for opening this issue here. I should have opened it directly at the kallisto github....had not had enough coffee yet to wake up...