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Search: Posts Made By: anna_
Forum: Bioinformatics 07-24-2012, 01:50 AM
Replies: 5
Views: 3,431
Posted By anna_
I don't know if you have the same problem than...

I don't know if you have the same problem than me. I could solve my problem finally by specifying the molecule type, the technique and the BioProject in the defline of the fasta file. Your fasta...
Forum: Bioinformatics 04-17-2012, 01:22 AM
Replies: 5
Views: 3,431
Posted By anna_
I am relpying to my own post: I think the...

I am relpying to my own post:

I think the old version of tbl2asn is not the problem. Instead:

The TSA NCBI page says I should include an assembly.cmt file with the argument -w assembly.cmt. As...
Forum: Bioinformatics 04-16-2012, 03:43 AM
Replies: 5
Views: 3,431
Posted By anna_
Exclamation current version of tbl2asn for linux

Hi,

I am trying to create an .sql file to upload it at NCBI TSA database. My input is a de novo assembly of approx. 20 000 contigs as .fsa. From the NCBI webpage I got the information that I...
Forum: Core Facilities 12-08-2011, 07:27 AM
Replies: 1
Views: 1,981
Posted By anna_
Question extracting scores from *.qual files HELP

Hi,

I want to extract the quality scores of certain contigs from a 454.qual-file. The file looks like this:

>contigs003410
27 27 30 64 64 64 64 64 64 64
64 64 64 64 64 19 64 64 64 64
64 64...
Forum: 454 Pyrosequencing 10-17-2011, 10:40 PM
Replies: 3
Views: 2,054
Posted By anna_
Thanks RCJK, but I know this link already....

Thanks RCJK,

but I know this link already. It says: Used Trimmed Length: the length of the part of the read newbler used.

So that means that theses lenght are the input for the assembly. So now...
Forum: 454 Pyrosequencing 10-17-2011, 05:23 AM
Replies: 3
Views: 2,054
Posted By anna_
trimmed length used; newbler

Hi,

in the newbler output file 454 trimStatus there are raw lenght, trimmed length and trimmed length used for each read.

Is this right:

raw lenght: length before image processing
trimmed...
Forum: Bioinformatics 02-25-2011, 06:01 AM
Replies: 8
Views: 5,417
Posted By anna_
Hi alex, I just wanted to say: It seems we...

Hi alex,

I just wanted to say: It seems we have very similar problems and no idea.

I didn't get your problem clearly enough, but I have a general advice:

Check all the out format options you...
Forum: Bioinformatics 02-23-2011, 12:08 AM
Replies: 20
Views: 23,833
Posted By anna_
kmcarr, another question about makeblastdb from...

kmcarr, another question about makeblastdb from anna again this time:

I should explain the procedure at first:

I'm searching for proteins that are related to drought stress in a huge conifer...
Forum: Bioinformatics 02-16-2011, 11:28 PM
Replies: 20
Views: 23,833
Posted By anna_
Thank you, it works. I feel quite a bit...

Thank you,

it works. I feel quite a bit ashamed because of my stupidity but I'll go on with asking and learning (hopefully), because I have no other choice.

thanks again!
Forum: Bioinformatics 01-13-2011, 05:56 AM
Replies: 20
Views: 23,833
Posted By anna_
Thank you both, I'm trying and the NBCI tool...

Thank you both,

I'm trying and the NBCI tool solution:

I use blast+. To get the text-file with the ID I used the command -outfmt "10 qgi". I when I use this output as the entry batch file I get...
Forum: Bioinformatics 01-11-2011, 06:17 AM
Replies: 4
Views: 3,825
Posted By anna_
Try to use "-hash_index" in your command. I don't...

Try to use "-hash_index" in your command. I don't exactly the reason, but I think this causes a kind referencing your database file.

anna
Forum: Bioinformatics 01-11-2011, 05:32 AM
Replies: 20
Views: 23,833
Posted By anna_
extract data from fasta-files with perl??

Hello,

I'm very knew to the subject and this is my first question ever:

I'm working with 454 data. I translated my contigs to protein sequences, created a blastdatabase with theses and used a...
Forum: Introductions 12-13-2010, 10:06 AM
Replies: 4
Views: 1,427
Posted By anna_
Sorry, I meant 500 000 reads (454)

Sorry, I meant 500 000 reads (454)
Forum: Introductions 12-13-2010, 10:03 AM
Replies: 4
Views: 1,427
Posted By anna_
Thanks for that quick comment. Our...

Thanks for that quick comment.
Our transcriptome has 500 000bp, the LargeContig FASTA-File has 7.5MB. I want to find protein coding sequences in there. The plan is to start with proteins from...
Forum: Introductions 12-13-2010, 08:59 AM
Replies: 4
Views: 1,427
Posted By anna_
Red face Don't know if I'm right

Hi everyone,

we have just sequenced a whole trancriptome of a conifer de novo and now it is my challenge to find candidate loci in there. I want to perform a stand alone blast search. I'm so new...
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