adaptercheck.py searches fastq files for potential
read-through contaminants in sequencing reads.
Where:
Run adaptercheck in the same folder as your read files.
Input:
Before running adaptercheck.py, select a single read file in
blreads to process eg. DL300_R1.fastq.
The file must be an uncompressed fastq file.
Parameters:
Adapters to find - Choose an adapter file, or
"custom adapter file"
adapter
file - If custom adapter, choose a fasta file containing
custom adapters
Size of
5' oligo - (default 12) It is often instructive to
re-run adaptercheck.py with a few different oligo sizes. The
frequency with which an oligonucleotide of k nt is
expected to occur within a long sequence is given in the
table below. For example, if a fastq file had reads totaling to
4 million nucleotides, an 11-mer would be expected to be seen
once by random chance. k-mers from the adapter used in
sequencing will usually occur several orders of magnitude more
frequently than background k-mers.
| k |
4k |
| 10 |
1,048,576 |
| 11 |
4,194,304 |
| 12 |
16,777,216 |
| 13 |
67,108,864 |
| 14 |
268,435,456 |
| 15 |
1,073,741,824 |
| 16 |
4,294,967,296 |
| 17 |
17,179,869,184 |
| 18 |
68,719,476,736 |
If you using adaptercheck.py to
determine which adapter was used for your reads, you may get
hits above background for more than one adapter in the list. Use
k=20, which will distinguish between adapters that differ within
the first 20 nt.
WHERE TO SEND OUTPUT - By default, the output will pop up
in a spreadsheet. If Text file is chosen send to an output file.
Output
file name - file to send report to
a spreadsheet, or to a .tsv file.
Output:
Output is written to the input directory.