About fake reads
From CSBLwiki
(Difference between revisions)
(Created page with '3.40) FAKE READS By "fake reads" I mean reads such as those created from a Genbank reference sequence or a consensus from some other assembly... or others for which there is no…') |
|||
| Line 2: | Line 2: | ||
By "fake reads" I mean reads such as those created from a Genbank | By "fake reads" I mean reads such as those created from a Genbank | ||
| + | |||
reference sequence or a consensus from some other assembly... or others | reference sequence or a consensus from some other assembly... or others | ||
| + | |||
for which there is no chromatogram (and there never was any | for which there is no chromatogram (and there never was any | ||
| + | |||
chromatogram). If you don't use any such reads, you can skip this | chromatogram). If you don't use any such reads, you can skip this | ||
| + | |||
step. | step. | ||
In the past, any read that ended with a .a2 or .c3 (where 2 and 3 | In the past, any read that ended with a .a2 or .c3 (where 2 and 3 | ||
| + | |||
could be any numbers), was considered a fake read. Now you can make | could be any numbers), was considered a fake read. Now you can make | ||
| + | |||
Autofinish not assume this using the .consedrc parameter (see CONSED | Autofinish not assume this using the .consedrc parameter (see CONSED | ||
| + | |||
CUSTOMIZATION): | CUSTOMIZATION): | ||
| Line 18: | Line 25: | ||
Instead, you must have determineReadTypes.perl put "fake" into the | Instead, you must have determineReadTypes.perl put "fake" into the | ||
| + | |||
"type:" field of a "template" WR item. See determineReadTypes.perl for | "type:" field of a "template" WR item. See determineReadTypes.perl for | ||
| + | |||
more information. | more information. | ||
Revision as of 08:19, 9 July 2010
3.40) FAKE READS
By "fake reads" I mean reads such as those created from a Genbank
reference sequence or a consensus from some other assembly... or others
for which there is no chromatogram (and there never was any
chromatogram). If you don't use any such reads, you can skip this
step.
In the past, any read that ended with a .a2 or .c3 (where 2 and 3
could be any numbers), was considered a fake read. Now you can make
Autofinish not assume this using the .consedrc parameter (see CONSED
CUSTOMIZATION):
consed.fakeReadsSpecifiedByFilenameExtension: false
Instead, you must have determineReadTypes.perl put "fake" into the
"type:" field of a "template" WR item. See determineReadTypes.perl for
more information.
