[mira_talk] Re: fn in paired-end reads?
- From: Sven Klages <sir.svencelot@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 31 May 2011 09:26:56 +0200
Hi Cleo,
2011/5/30 Cleo HC Ho <cleoho175@xxxxxxxxx>
> Hi all,
>
> After the SSAHA2 extraction, some reads are tagged with fn. What does "fn"
> mean? I tried searching the archive but did not find anything. Thanks in
> advance!
>
You have splitted paired-end data using sff_extract?
Taken from sff_extract:
Splits a paired end read and writes sequences into FASTA, FASTA qual
and XML traceinfo file. Returns the number of sequences created.
As the linker sequence may be anywhere in the read, including the ends
and overlapping with bad quality sequence, we need to perform some
computing and eventually set new clip points.
If the resulting split yields only one sequence (because linker
was not present or overlapping with left or right clip), only one
sequence will be written with ".fn" appended to the name.
If the read can be split, two reads will be written. The side left of
the linker will be named ".r" and will be written in reverse complement
into the file to conform with what approximately all assemblers expect
when reading paired-end data: reads in forward direction in file. The
side
right of the linker will be named ".f"
If SSAHA found partial linker (linker sequences < length of linker),
the sequences will get a "_pl" furthermore be cut back thoroughly.
If SSAHA found multiple occurences of the linker, the names will get an
additional "_mlc" within the name to show that there was "multiple
linker contamination".
For multiple or partial linker, the "good" parts of the reads are
stored with a ".part<number>" name, additionally they will not get
template information in the XML
hth,
Sven
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