1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
|
.. _process_qseq:
.. index:: process_qseq.py
*process_qseq.py* -- Given a directory of per-swath qseq files, this script generates a single fastq per lane.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
**Usage:** :file:`process_qseq.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-input_dir
The input directory
-o, `-`-output_dir
The output directory
-r, `-`-read
The read number to consider
**[OPTIONAL]**
-l, `-`-lanes
The lane numbers to consider, comma-separated [defaut: 1,2,3,4,5,6,7,8]
-b, `-`-bases
The number of bases to include (useful for slicing a barcode) [defaut: all]
`-`-ignore_pass_filter
Ignore the illumina pass filter [default:False; reads with 0 in pass filter field are discarded]
**Output:**
Generate fastq files from all lanes of read 1 data in the current directory.
::
process_qseq.py -i ./ -o ./fastq/ -r 1
Generate fastq files from all lanes of read 2 data in the current directory, truncating the sequences after the first 12 bases.
::
process_qseq.py -i ./ -o ./fastq/ -r 2 -b 12
|
