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Search: Posts Made By: simonandrews
Forum: Bioinformatics 04-26-2011, 03:07 AM
Replies: 14
Views: 3,096
Posted By simonandrews
It looks like you have a load of lines where...

It looks like you have a load of lines where there is an extra line break in the header line. This will cause the next line (which should be the sequence) to actually be the second part of the...
Forum: Bioinformatics 04-25-2011, 11:57 PM
Replies: 14
Views: 3,096
Posted By simonandrews
You could try the following script (only lightly...

You could try the following script (only lightly tested) which should find any oddly formatted entries in your file and remove them. Hopefully it should leave you with a file which you can process....
Forum: Bioinformatics 04-21-2011, 12:02 AM
Replies: 14
Views: 3,096
Posted By simonandrews
Did you see the note I posted yesterday? There's...

Did you see the note I posted yesterday? There's not much else anyone here can do - you need to figure out what the formatting problem in your csfasta file is. Try searching with a small section...
Forum: Bioinformatics 04-20-2011, 04:45 AM
Replies: 14
Views: 3,096
Posted By simonandrews
This seems to be the relevant error. The program...

This seems to be the relevant error. The program doesn't like the format of your csfasta file. This could be something as simple as their being a blank line somewhere in the file, it could be that...
Forum: Bioinformatics 04-19-2011, 03:46 AM
Replies: 14
Views: 3,096
Posted By simonandrews
You don't want to remove the dots. Those are...

You don't want to remove the dots. Those are locations in your read where the color could not be determined (equivalent to an N in base space). Removing the dots will create deletions which won't...
Forum: Bioinformatics 04-18-2011, 11:38 PM
Replies: 14
Views: 3,096
Posted By simonandrews
You'd need to use abi-dump from the sra-toolkit...

You'd need to use abi-dump from the sra-toolkit (http://www.ncbi.nlm.nih.gov/books/NBK47540/#SRA_Download_Guid_B.3_Installing_the_Too).
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