Hi.
The usage of optional output arguments are not very clear.
After several tests, I found eastr takes those junction outputs as files not PATH.
The correct usage should be something like:
--out_original_junctions ${outdir}/original_junc.bed \
--out_kept_junctions ${outdir}/valid_junc.bed \
--out_removed_junctions ${outdir}/removed_junc.bed \
On the other hand, --out_filtered_bam takes the PATH and it will create the dir. --removed_alignments_bam is a flag which will automatically add _removed_alignments as the defined suffix in advance.
The description in the document is a little bit confusing... Just a reminder for other users.
I don't know if the behavior remains the same in python version. I am using cpp version, thus put this issue here.
Hi.
The usage of optional output arguments are not very clear.
After several tests, I found eastr takes those junction outputs as files not PATH.
The correct usage should be something like:
On the other hand,
--out_filtered_bamtakes the PATH and it will create the dir.--removed_alignments_bamis a flag which will automatically add _removed_alignments as the defined suffix in advance.The description in the document is a little bit confusing... Just a reminder for other users.
I don't know if the behavior remains the same in python version. I am using cpp version, thus put this issue here.