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Forum: Bioinformatics 03-23-2014, 06:18 PM
Replies: 2
Views: 1,004
Posted By Dagga
Script to find common/unique CDS between two genomes

Hi All,

I was wondering if anyone could suggest a script that would allow me to comparatively analyse two genomes.

I was hoping I could use the gene (or protein) list of two organisms and input...
Forum: Bioinformatics 03-14-2014, 02:16 AM
Replies: 52
Views: 22,372
Posted By Dagga
Thanks for the tips! I have finally got this...

Thanks for the tips! I have finally got this program working.

I was wondering if anyone has any tips on a starting region for the error settings that are inputted into the library file.

I have...
Forum: Bioinformatics 03-11-2014, 12:47 PM
Replies: 5
Views: 1,609
Posted By Dagga
Thanks! I did plan on reassembling the new...

Thanks!

I did plan on reassembling the new data but there seems to be contamination and this making a poor assembly. It is this reason that I wanted to use the old assembly to caputure the reads...
Forum: Bioinformatics 03-10-2014, 10:11 PM
Replies: 5
Views: 1,609
Posted By Dagga
Expanding the coverage of an old assembly

Hi,

I sequenced the genome of an organism a few years ago and got an ok assembly (~100 contigs but many regions with N's).

Recently, we re-sequenced the genome of the same organism and I would...
Forum: Bioinformatics 03-06-2014, 04:56 PM
Replies: 3
Views: 1,090
Posted By Dagga
Hi All, The I have assembled both sets of...

Hi All,

The I have assembled both sets of data individually and it seems the data for the second run is not as good as there is some contamination. So I have a further question.

If I was going...
Forum: Bioinformatics 03-06-2014, 04:45 PM
Replies: 1
Views: 1,795
Posted By Dagga
Script to replace space with underscore using CLI

Hi,

I was hoping I could help with 2 scripts to perform similiar functions.

I have a fasta file that is a combination of all the genome sequences from a specific phylum. I was hoping I could...
Forum: Bioinformatics 02-19-2014, 02:06 PM
Replies: 3
Views: 1,090
Posted By Dagga
Best way to perform assembly with two sets of raw data

Best way to merge data from two separate sequence runs
Hi,

We have performed 2 sequencing runs of a bacterial organism with a genome about 4.4Mb. One was performed a few years ago by BGI and we...
Forum: Bioinformatics 02-19-2014, 03:21 AM
Replies: 1
Views: 711
Posted By Dagga
Are velvet 'auto' setting parameters reliable?

Hi,


I have just begun assembling genomes with velvet. I am new to de novo assembly and have been told the "auto" setting for -cov_cutoff and -exp_cov parameters are reliable for use. However, I...
Forum: Bioinformatics 02-18-2014, 02:38 PM
Replies: 9
Views: 1,563
Posted By Dagga
Thanks!! I appreciate it!

Thanks!! I appreciate it!
Forum: Bioinformatics 02-17-2014, 04:31 PM
Replies: 11
Views: 1,929
Posted By Dagga
Great! thanks GenoMax i'll give that a try.

Great!

thanks GenoMax i'll give that a try.
Forum: Bioinformatics 02-17-2014, 04:21 PM
Replies: 11
Views: 1,929
Posted By Dagga
and its > 90% N's for about 15 contigs. These are...

and its > 90% N's for about 15 contigs. These are the very large contigs with a length of 15-50 Mbp...

The other contigs seem normal.
Forum: Bioinformatics 02-17-2014, 04:19 PM
Replies: 11
Views: 1,929
Posted By Dagga
I have a feeling the insert length could be an...

I have a feeling the insert length could be an issue. We have used an Nextera prep and according to the sequencing centre - this has a variable insert length. I am attempting to reassemble with a set...
Forum: Bioinformatics 02-17-2014, 03:15 PM
Replies: 11
Views: 1,929
Posted By Dagga
I think I have found the reason why the...

I think I have found the reason why the contigs.fa files are so large - but I am still not sure how to fix it.

I managed to open one of the smaller contigs.fa files (0.5gig) and have found there...
Forum: Bioinformatics 02-17-2014, 12:35 PM
Replies: 9
Views: 1,563
Posted By Dagga
Excellent! Whilst this does help with some...

Excellent!

Whilst this does help with some genomes that I am assembling right now, we have some older genomes that were sequenced by BGI and these contain N's that we still need to have removed...
Forum: Bioinformatics 02-17-2014, 12:16 PM
Replies: 9
Views: 1,563
Posted By Dagga
TiborNagy: Sorry, the file will be in fasta...

TiborNagy: Sorry, the file will be in fasta format post de novo assembly.

would you be able to alter the script to handle contig names please?

Thanks!
Forum: Bioinformatics 02-17-2014, 02:15 AM
Replies: 9
Views: 1,563
Posted By Dagga
Thanks for that!! Will this rename the...

Thanks for that!!

Will this rename the contigs?

Will the contig that is split be called the same thing in contig1.txt and contig2.txt.

Is it possible to rename the contigs when they are...
Forum: Bioinformatics 02-16-2014, 11:55 PM
Replies: 11
Views: 1,929
Posted By Dagga
I dont think it is repetitive and it is a...

I dont think it is repetitive and it is a bacterial genome so it should be relatively simple. I havent dont a dotplot but I think there would be a few differences to the other genome so i dont think...
Forum: Bioinformatics 02-16-2014, 02:58 PM
Replies: 9
Views: 1,563
Posted By Dagga
Remove N's and split contigs

Hi,

I have some genomes that I will be uploading to NCBI soon. I have been told that all N's need to be removed and the contigs split at this position.

I am new to command line interface so I...
Forum: Bioinformatics 02-16-2014, 02:11 PM
Replies: 11
Views: 1,929
Posted By Dagga
Thanks! Yep! I am sure they are in the gig...

Thanks!

Yep! I am sure they are in the gig size but they range from 20-50 gigs depending on the kmer setting of velvet. As far as I know, it is the latest version of velvet (v 1.2.10).

All of...
Forum: Bioinformatics 02-13-2014, 08:35 PM
Replies: 11
Views: 1,929
Posted By Dagga
Very large contig files using Velvet

Hi,

I have just begun assembling some genomes using velvet using a range of kmer lenghts (a gap of 10 between kmer length of 25-179). For all of these files I am generating very large contigs.fa...
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