Hello,
I am trying to generate comparison files (crunch files) to view in ACT. I am using the example code below in the terminal:
makeblastdb -in NC_011748.fasta -dbtype nucl
blastn -query SRR292770_single.fasta -db NC_011748.fasta -evalue 1 -task megablast -outfmt 6 > SRR292770_NC_011748.crunch
I am able to generate the crunch files using the my fasta files but when I try to load my .gbk file into ACT i get the following message:
"comparison file read failed: out of range error: match goes off end of query sequence 319884
I am successful when I load my crunch file with my seq.fasta file and the reference.gb file (downloaded from NCBI) however I get the aforementioned error message using the .gbk file that I received from MicrobesNG
Thanks Sarah
0 answers
No answers yet.
Log in to answer this question.
-
Crunch file for Artemis Comparison Tool
written by SushiRoll •
-
Problems to generate crunch files
written by mcecis •
-
Wrong feature labels when using BRIG tool
written by deshpandenandan1975 •
-
Artemis Comparison Tool "error while reading: cannot understand comparison file format"
written by jleehan •
-
Blast locally on multiple fasta files with multiple database
written by fec2 •
-
FASTA to SAM for Tablet Assembly Visulisations
written by peflanag •
-
Extract specific fasta sequences from multiple multi-fasta files located in a directory using Perl.
written by MB •
-
Problems with using WebACT to create crunch files for ACT
written by dadarotimi •
-
WebACT not returning result
written by samuelksm •
-
How To Create Genbank File(.Gbk/.Gb) Format From Multi-Fasta Format File?
written by Kits •
It appears that the two GenBank files are different. Specifically, it seems that a file from
MicrobesNGis shorter. If this is the file you need, convert it to FASTa, do the search with it, and it should work afterwards. Alternatively, go with whatever works already.