SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 34
Search took 0.00 seconds.
Search: Posts Made By: dina
Forum: Bioinformatics 11-06-2015, 06:46 AM
Replies: 1
Views: 831
Posted By dina
454 assembly genome size

How does the newbler algorithm difined the estimated genome size?
Forum: Events / Conferences 09-10-2010, 01:08 AM
Replies: 15
Views: 8,829
Posted By dina
still availabe?

Hi ECO,
Is there any chance one of the conferences is still available?
THANKS!!!
Forum: Sample Prep / Library Generation 08-18-2010, 03:10 AM
Replies: 3
Views: 2,780
Posted By dina
library

hi
sorry for the late reply, I was on a vacation. I ment we receive very low concentrations of cDNA immediately after the rapid protocol
Forum: Sample Prep / Library Generation 07-25-2010, 12:39 AM
Replies: 3
Views: 2,780
Posted By dina
bad library prep results

Hi,
Has anyone encountered a problem in the rapid protocol of 454? We have a good cDNA, but after the rapid protocol nothig is left,,,,
Thank you!
Forum: Bioinformatics 07-19-2010, 04:38 AM
Replies: 3
Views: 1,817
Posted By dina
homopolimers

say 30 long, but not neccessary.. ?
Forum: Bioinformatics 07-18-2010, 12:54 PM
Replies: 3
Views: 1,817
Posted By dina
454 accuracy with homopolymers

I wanted to know what is the accuracy of 454 with homopolymers ?
Forum: Bioinformatics 07-11-2010, 10:26 PM
Replies: 16
Views: 5,671
Posted By dina
splitting to mids on both sides

Hi Robs,
Thank you, but I saw that if I use for example: mid2@sffFile, then all the samples with mid2 at the beginning will be chosen, so how do I define to sfffile just to present all the options...
Forum: 454 Pyrosequencing 07-11-2010, 11:50 AM
Replies: 2
Views: 1,421
Posted By dina
running amplicons together with non amplicon lanes

Hi,
I wanted to know whether is is ok to use one plate in which some regions are for amplicons and others are not. If so, what kind of run should it be? Image processing only ?
Forum: 454 Pyrosequencing 07-11-2010, 11:48 AM
Replies: 0
Views: 1,819
Posted By dina
low cDNA concentration after the RAPID protocol

Hello,
We receive low concentrations of cDNA after fragmentation. Has anybody here encountered this problem? Could the problem be in the fragmentation solution? Do you prepare a fresh one each time?
Forum: Bioinformatics 07-11-2010, 11:33 AM
Replies: 16
Views: 5,671
Posted By dina
spliting to mids- with mids on both sides

Hi.
I need help with splitting my reads to the samples they refer to, but each sample was tagged with a mid at the 5' end and at the 3' end . for example: sample 1 is tagged with mids 1 at the...
Forum: Bioinformatics 07-06-2010, 09:03 PM
Replies: 4
Views: 2,105
Posted By dina
I meant that I use the AVA software, enter a ...

I meant that I use the AVA software, enter a reference and primers and planning the multiplexer. I have 30 samples. Then I receive the variations, but only in 2 samples. I thought it was because...
Forum: Bioinformatics 07-06-2010, 08:12 PM
Replies: 4
Views: 2,105
Posted By dina
1.how exactly to use sffile to split the samples?...

1.how exactly to use sffile to split the samples?
2.I meant that I have very variable amplicons, when I enter a reference, most samples are not represented in the variations,,,,
Thank you a lot!
Forum: Bioinformatics 07-06-2010, 11:19 AM
Replies: 4
Views: 2,105
Posted By dina
454 Amplicons-no reference

Hello,
I wanted to know whether there is some option to analyze amplicon run with many samples barcoded with MIDs if I only have the primers and not the reference? Is it possible with the 454...
Forum: Bioinformatics 03-05-2010, 12:05 AM
Replies: 1
Views: 1,611
Posted By dina
BLAt

Hi,
I have a strange problem: some of the contigs receive exact match in blast but when usin blat there is a big gap which might be interesting for me ( a mutation? a big part of the gene is...
Forum: Bioinformatics 02-27-2010, 08:20 PM
Replies: 3
Views: 6,661
Posted By dina
sff extract

Hi
How can I extract sff files? only in linux or windows is possible too?
Forum: Bioinformatics 11-07-2009, 07:10 AM
Replies: 8
Views: 6,562
Posted By dina
refseq genomic vs.nr/nt

ok, I understood why it happens. It depends if the database is refseq_genomic or nr/nt. when I use nr/nt only a small region of the contig is found. When I use refseq genomic, the whole contig...
Forum: Bioinformatics 11-07-2009, 02:52 AM
Replies: 8
Views: 6,562
Posted By dina
blast

I now noticed that if I do blsat through the viewmapper of the ncbi I receive the same result as in blat ( the whole contig from existent sequencing data), but if I blast via the regular blast I...
Forum: Bioinformatics 11-07-2009, 01:43 AM
Replies: 8
Views: 6,562
Posted By dina
blast vs. blat-continued

I tried the blast with and without the filter and the result was the same; for a 1500 bp contig blast finds only the last 300 bp (this is the only hit) while blat finds the whole contig,,,
Forum: Bioinformatics 11-06-2009, 01:01 AM
Replies: 8
Views: 6,562
Posted By dina
blat vs. blast

Hello,
As I was advised here I tried blat instead of lst and I was really surprised. For example I checked a 1500 bp contig, and while blast found only very partial hit (about 300 bp), blat found a...
Forum: Bioinformatics 11-05-2009, 11:30 AM
Replies: 3
Views: 2,024
Posted By dina
Blat

Thank you. Can you explain to me how do I run BLAT for mant contigs as abatch? how I can do that via the command line and not on the web? Thank you!
Forum: Bioinformatics 11-04-2009, 11:30 PM
Replies: 3
Views: 2,024
Posted By dina
blast of the 454 reads

Hi
I want to find virus integration sites in a genome we sequenced. Is it more reasonable to blast the resulted contigs or maybe blast the reads themselves would be more productive?
Do you have...
Forum: Bioinformatics 11-02-2009, 09:23 AM
Replies: 5
Views: 4,310
Posted By dina
blast

It happens for about 10% of the reads. I guess it is indeed because the quality of the read.
another question about blast: when I run it with this command:megablast, I receive in the end a big html...
Forum: Bioinformatics 11-01-2009, 11:28 PM
Replies: 5
Views: 4,310
Posted By dina
blast

Than you for your reply, I'm using the command:
megablast -b -1 -m 9 -i mapping/454AllContigs.fna -d /root/genome_annotation/blast/ncbi_nt/nt>blastout.txt

There are different contigs some are...
Forum: Bioinformatics 11-01-2009, 06:25 AM
Replies: 5
Views: 4,310
Posted By dina
blast of the contigs

Hello,
I've sequenced a genome and received contigs. I'm trying to blast the contigs using megablast installed locally on our computer. For many of the contigs I receive the error message: could not...
Forum: Bioinformatics 10-26-2009, 04:22 AM
Replies: 3
Views: 3,076
Posted By dina
tsv

yes, I tried this , but it wouldn't work. Maybe the file is too big..
So, is there any other way to export the HCdiffs table ?
Showing results 1 to 25 of 34

 


All times are GMT -8. The time now is 11:24 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO