Re^2: how to create output file using perl

First I downloaded all the est fasta sequences of tomato from NCBI.Then I submit that sequence file into an online tool EGassembler for sequence cleaning,vector masking,repeat masking,organelle masking and sequence assembly..As a result I got this contig file..This contig file is used for offline local blast..For doing blastn I downloaded the genome of Arabidopsis thaliana.Then I run the blast..

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Re^3: how to create output file using perl by 1nickt (Canon) on Jul 02, 2015 at 09:31 UTC
Nice, sounds like a fun project! So it sounds like the contig file is produced correctly. And it runs "the blast" correctly on the first and the last "contig" in the file. But not on the 2nd or 3rd. Sounds like there is a problem passing the individual "contig" sections to the "blatster." Have you tried manually splitting up the contig file into smaller pieces and passing them to the blaster? If you cut the file in half and passed #1 + #2 in one file and #3 + #4 in another, and both those files processed correctly, you might conclude that the error is in how you pass the files. If you do that and still #2 and #3 don't process, you might conclude that there is bad data in those contigs. How does the blaster report if it finds an error in the input data? Remember: Ne dederis in spiritu molere illegitimi!	[reply] [d/l]

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Re^3: how to create output file using perl
by 1nickt (Canon) on Jul 02, 2015 at 09:31 UTC

Nice, sounds like a fun project!

So it sounds like the contig file is produced correctly. And it runs "the blast" correctly on the first and the last "contig" in the file. But not on the 2nd or 3rd.

Sounds like there is a problem passing the individual "contig" sections to the "blatster."

Have you tried manually splitting up the contig file into smaller pieces and passing them to the blaster? If you cut the file in half and passed #1 + #2 in one file and #3 + #4 in another, and both those files processed correctly, you might conclude that the error is in how you pass the files. If you do that and still #2 and #3 don't process, you might conclude that there is bad data in those contigs.

How does the blaster report if it finds an error in the input data?

Remember: Ne dederis in spiritu molere illegitimi!

[reply]
[d/l]