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Hello!
I just realized I should have posted this to this forum, so here it is again, sorry!
I am a graduate student at UC Berkeley currently working with raw reads of several transcriptomes in an attempt to find and assemble reads that match a couple of genes I'm studying. This site has already been very useful to me (Thank you!!!!), but I haven't found any answers pertaining to my current problem.
I was hoping I could get some help with a BLAST problem I'm having. I am working with standalone blast, and am building blast databases from fasta files of transcriptome raw reads. I have successfully used the command:
makeblastdb -in COST_1_final.fasta -input_type fasta -dbtype nucl -out COST_1_final for several fasta files of raw reads (with varying names of course) but a few of the files result in multiple sets of database files, marked for example <filename>.00.nhr and <filename>.01.nhr with what I believe is an alias file <filename>.nal
The command as it runs give the usual message:
Building a new DB, current time: 10/15/2015 10:49:55
New DB name: COST_u_final
New DB title: COST_u_final.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 16313457 sequences in 937.429 seconds.
but then results in multiple sets of files.
Any ideas about how I can make just one set of database files, as has successfully happened with the rest of my fasta files? I would really appreciate any help!!
I just realized I should have posted this to this forum, so here it is again, sorry!
I am a graduate student at UC Berkeley currently working with raw reads of several transcriptomes in an attempt to find and assemble reads that match a couple of genes I'm studying. This site has already been very useful to me (Thank you!!!!), but I haven't found any answers pertaining to my current problem.
I was hoping I could get some help with a BLAST problem I'm having. I am working with standalone blast, and am building blast databases from fasta files of transcriptome raw reads. I have successfully used the command:
makeblastdb -in COST_1_final.fasta -input_type fasta -dbtype nucl -out COST_1_final for several fasta files of raw reads (with varying names of course) but a few of the files result in multiple sets of database files, marked for example <filename>.00.nhr and <filename>.01.nhr with what I believe is an alias file <filename>.nal
The command as it runs give the usual message:
Building a new DB, current time: 10/15/2015 10:49:55
New DB name: COST_u_final
New DB title: COST_u_final.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 16313457 sequences in 937.429 seconds.
but then results in multiple sets of files.
Any ideas about how I can make just one set of database files, as has successfully happened with the rest of my fasta files? I would really appreciate any help!!
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