Running velocyto on bulk RNA

[lldelisle]

Hello,
I would like to run velocyto on a time series of bulk RNA-seq. Each time point is 24 hours apart. I did the alignment with STAR and as it is a first strand library I reversed the strand of mapping in the bam (see at the end) to be able to use the default logic.
When I looked at the arrows on the PCA, they are not really intuitive. Did I make something wrong? I tried to check with the circadian dataset which is used in the publication but as it is solid data I could not map them...
Many thanks,
Lucille
To reverse the strand I did:
samtools view -h $b | awk -v OFS="\t" '{if($1~/^@/){print}else{n=$2;d=16;q=(n-n%d)/d+(n<0);if(q%2==1){$2-=d}else{$2+=d};print}}' | samtools view -b - > ${b}_reversed.bam