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Search: Posts Made By: Linnea
Forum: Bioinformatics 12-12-2016, 01:01 AM
Replies: 11
Views: 8,063
Posted By Linnea
If you want to keep Windows as your system but...

If you want to keep Windows as your system but use linux from time to time I recommend installing VirtualBox and running Ubuntu as a virtual machine. I've been using it for a year on my laptop and it...
Forum: Bioinformatics 08-19-2015, 11:03 PM
Replies: 6
Views: 1,719
Posted By Linnea
I also agree, first try to get the mitochondrial...

I also agree, first try to get the mitochondrial reads.

We had exactly thee same problem when assembling our non-model organism (1Gb, mitochondrion ~16kb), and didn't get any mitochondrial contigs...
Forum: De novo discovery 08-19-2015, 04:27 AM
Replies: 2
Views: 2,586
Posted By Linnea
It's not outside [LIB], it's a second library...

It's not outside [LIB], it's a second library that is defined! So for every library you have, you start with a line "[LIB]", and then list all the parameters (specific for each library).
In the...
Forum: Bioinformatics 07-14-2015, 11:20 PM
Replies: 2
Views: 2,043
Posted By Linnea
Hi, For the ChrY I would actually suggest...

Hi,

For the ChrY I would actually suggest that you assemble the male reads instead, then map the female reads and define the ones with zero female read coverage as Y scaffolds. Doing the other way...
Forum: SOLiD 07-01-2015, 02:52 AM
Replies: 5
Views: 7,024
Posted By Linnea
No sorry, I can't explain that part, maybe...

No sorry, I can't explain that part, maybe someone else has an idea?

But actually, why can't they just be real indels with a very high quality? (99 seems to be the highest quality you can get:...
Forum: SOLiD 06-29-2015, 10:39 PM
Replies: 5
Views: 7,024
Posted By Linnea
Hello Daniele, To at least partly answer...

Hello Daniele,

To at least partly answer your question: HaplotypeCaller performs local realignment within the run, so your "final bam file" is actually not the one you input to HaplotypeCaller but...
Forum: Bioinformatics 09-16-2013, 10:01 PM
Replies: 2
Views: 3,555
Posted By Linnea
Thanks for your reply, actually that was the...

Thanks for your reply, actually that was the result from grep.. so no other mappings.

However, I think I've just found the problem anyway.. When I checked if the fastq files were sorted properly,...
Forum: Bioinformatics 09-13-2013, 04:16 AM
Replies: 2
Views: 3,555
Posted By Linnea
Exclamation bwa-mem paired reads problem

Hi,

I have aligned several re-sequenced individuals (Illumina HiSeq, paired-end with IS ~450bp) to a draft assembly, and when looking at the alignments in IGV, it seemed like almost all of them...
Forum: Bioinformatics 06-16-2013, 11:08 PM
Replies: 6
Views: 4,545
Posted By Linnea
Did you get "[LIB] command" not found? First I...

Did you get "[LIB] command" not found? First I read "[LIB] not found" and interpreted it as SOAP didn't find the fastq file - I had that problem and it helped when I added the full path instead of...
Forum: De novo discovery 05-02-2012, 06:38 AM
Replies: 18
Views: 13,713
Posted By Linnea
Hi shal, It is very hard to say in advance...

Hi shal,

It is very hard to say in advance how much data you will need for a making a denovo assembly of a particular organism.. It not only depends on the genomic content (especially repeats,...
Forum: Bioinformatics 04-26-2012, 04:03 AM
Replies: 4
Views: 1,892
Posted By Linnea
Have you tried GapCloser from the SOAP package? I...

Have you tried GapCloser from the SOAP package? I could close/remove ~80% of the Ns in a 1Gb draft assembly by using paired end reads with inserts of 200-500bp.

Of course, whether it will work or...
Forum: General 05-09-2011, 10:11 PM
Replies: 2
Views: 1,212
Posted By Linnea
Check out Ensembl BioMart: ...

Check out Ensembl BioMart:

http://www.ensembl.org/biomart/martview/f1db9f58deeb4381715a6b8d132e9d21/f1db9f58deeb4381715a6b8d132e9d21

You can choose if you want coding sequence, exons, cDNA,...
Forum: Bioinformatics 02-21-2011, 10:26 PM
Replies: 2
Views: 2,960
Posted By Linnea
I suppose you don't have a close relative which...

I suppose you don't have a close relative which you could map your reads on?

Do you have some paired end data? We assembled all paired end data first, and then mapped all mate pairs onto the...
Forum: Bioinformatics 10-29-2010, 05:41 AM
Replies: 13
Views: 4,725
Posted By Linnea
So you can actually align 454 reads (that has not...

So you can actually align 454 reads (that has not been aligned before) to an assembly with consed? I thought it was more for viewing. Sounds interesting! I don't have the assembly in ace, but it...
Forum: Bioinformatics 10-28-2010, 04:04 AM
Replies: 13
Views: 4,725
Posted By Linnea
SOAP GapCloser not for 454 reads

I just tested GapCloser on my 454 reads, and it failed saying "read max length should be less than 188bp". So actually it is not working with 454 reads at all (since most of them are much longer than...
Forum: Bioinformatics 10-25-2010, 10:39 PM
Replies: 13
Views: 4,725
Posted By Linnea
Could you provide GapCloser with 454 reads, even...

Could you provide GapCloser with 454 reads, even if the original assembly is done by illumina?? I have never tried it, but if this is possible I'll certainly give it a shot!
Forum: Bioinformatics 10-20-2010, 05:12 AM
Replies: 13
Views: 4,725
Posted By Linnea
The problem is that I don't have a decent 454...

The problem is that I don't have a decent 454 coverage...:(
The Illumina coverage is ~30X, while for the 454 I only have 1X (it's only a test run, and no more runs are planned.. When I assembled...
Forum: Bioinformatics 10-19-2010, 06:05 AM
Replies: 13
Views: 4,725
Posted By Linnea
Improving Illumina assembly with 454 reads?

Hi all,

I'm working on a large genome assembly (~1Gbp) with Illumina paired-end reads, and currently I'm down to ~90 000 scaffolds (N50=26kb). Now I've got some additional 454 data (single end),...
Forum: De novo discovery 08-30-2010, 03:16 AM
Replies: 0
Views: 1,765
Posted By Linnea
Question Chromosome assembly with next-gen data?

Hey all,

I've just seen that the Turkey and Panda genomes (assembled from 454+Illumina reads and only Illumina reads respectively) now are up on Pre Ensembl with complete chromosomes.

The...
Forum: Illumina/Solexa 06-08-2010, 11:46 PM
Replies: 2
Views: 4,975
Posted By Linnea
Thanks for the reply! I hadn't seen that...

Thanks for the reply!

I hadn't seen that SamplePrep guide. Then we'll go for 36bp!

Yes, we're doing de novo and we allready have two full flowcells sequenced with paired-ends, so the current...
Forum: Illumina/Solexa 06-07-2010, 05:28 AM
Replies: 2
Views: 4,975
Posted By Linnea
Read length for Illumina mate pairs

Hey all,

I've heard that with the new, longer Illumina reads (>100bp), for mate-pair sequencing the amount of chimeric reads has increased strikingly. (Because it is much more likely to read over...
Forum: Bioinformatics 04-13-2010, 05:13 AM
Replies: 13
Views: 6,357
Posted By Linnea
"Very short reads" refers to the sequencing...

"Very short reads" refers to the sequencing technique, not the organism. I would guess very short reads in this case are Illumina and SOLiD reads, up to ~75-100 bp.
Oases should be fine to use with...
Forum: Introductions 03-08-2010, 06:03 AM
Replies: 373
Views: 132,605
Posted By Linnea
Greetings from Uppsala

Hi!

I am a recently graduated bioinformatician and have just started working as a research engineer. I am trying to de novo assembly transcriptome Solexa sequences but am a newbie to this by all...
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