Last updated: 2015-04-11

Code version: 3275cbc6932e4def9f737a536299aa2022c5c7a1

The second of four flow cells was sequenced at the Functional Genomics Facility (FGF). Here is the message from Pieter Faber:

We finished Flowcell #2 of your Illumina sequencing experiment (4 flowcells SR100). No technical problem were encountered. I attached several QC files in support.

I have uploaded the data in fastq format to the Genomics Core ftp server data server (gilad Lab folder, folder = /gilad/NGS/150327_700819F_0304_AC6WURACXX-YG-SR100-FC-2).

To download, need to preface /NGS with /Genomics_Data.

cd /mnt/gluster/data/internal_supp/singleCellSeq/raw
nohup wget --user=gilad --password='<password>' -r &
mv nohup.out 150327_700819F_0304_AC6WURACXX-YG-SR100-FC-2.log

The download took ~10 hours. It started at 22:33:05 and ended at 08:38:19. However, wget reported that it only took ~5 hours. Here’s the final line of output:

Downloaded: 1377 files, 101G in 5h 0m 56s (5.71 MB/s)

To remove the unnecessary directories from the FGF FTP site, I moved the files.

mv 150327_700819F_0304_AC6WURACXX-YG-SR100-FC-2
rmdir -p

Next I removed the extraneous CASAVA directories and added the flow cell name to the filename.

cd -

I did this with the following Python code:

import glob
import shutil

files = glob.glob('raw/150327_700819F_0304_AC6WURACXX-YG-SR100-FC-2/FastQ/Project_YG-SR100-2/Sample*/*fastq.gz')

target_dir = 'fastq/'
log = open('rearrange_C6WURACXX.log', 'w')

for f in files:
    path = f.strip('fastq.gz').split('/')
    flow_cell = path[1].split('_')[-1][1:10]
    file_parts = path[-1].split('_')[:-1]
    new_name = target_dir + '.'.join(file_parts + [flow_cell]) + '.fastq.gz'
    log.write(f + '\t' + new_name + '\n')
    shutil.move(f, new_name)