Schumer lab: Download data to Sherlock from UW (PacBio)
Download data with Globus
1) info for JJ to fill in
the important files are *hifi_reads.bc*.bam and *hifi_reads.bc*.bam.pbi
- download all pacbio data from globus. the important files are *hifi_reads.bc*.bam and *hifi_reads.bc*.bam.pbi
Delete unnecessary files
1) delete fail_reads/ directory and unassigned.bam files
cd /path/to/parent/directory/
rm -r fail_reads/
rm hifi_reads/*.hifi_reads.unassigned.bam*
Rename files
The files we get back from UW are named using a unique barcode that they assign, but is meaningless to us. We want to rename all of these files based on the sample names we provided them. The information connecting barcodes to sample names can be found in the SequencingReport.pdf that they send (e.g. 240724_UW_LongRead_SequencingReport_Baczenas.J(Stanford).pdf).
2) copy the renaming script to the directory with reads
cd /path/to/directory/with/reads/
cp /home/groups/schumer/shared_bin/Lab_shared_scripts/rename_PacBio_UW_reads.sh .
3) make a file called sample.key which contains the UW barcodes and the sample name, separated by "@".
$ cat sample.key
bc2008@Xvar-JUCH-6-V-24-S265-M-01
bc2014@Xvar-JUCH-6-V-24-S178-M-01
bc2015@Xvar-JUCH-6-V-24-S250-M-01
bc2016@Xvar-JUCH-6-V-24-S250-M-02
3) run the renaming. it should take ~3 min per sample
sh rename_PacBio_UW_reads.sh
4) you are all done!
