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Forum: RNA Sequencing 10-12-2017, 10:40 PM
Replies: 2
Views: 1,209
Posted By jvanleuven
Thank you for the paper. Below are several more...

Thank you for the paper. Below are several more that address the issue.
I'm still not sure if we should pick a method or use some agglomeration of them.

Seyednasrollah F, Laiho A, Elo LL. 2015....
Forum: RNA Sequencing 10-12-2017, 04:02 PM
Replies: 2
Views: 1,209
Posted By jvanleuven
Inconsistent gene lists: DESeq2, EdgeR, CuffDiff, and homemade glm

Hello,
In an effort to get a reliable list of DEGs, I ran CuffDiff, EdgeR, and DESeq2. I though I would grab the overlapping genes and be good to go. However, the DEG lists outputted by each were...
Forum: Bioinformatics 01-08-2013, 05:50 AM
Replies: 4
Views: 1,323
Posted By jvanleuven
Yes. Mate pair. I haven't decided yet...

Yes. Mate pair.

I haven't decided yet whether to write some software to handle these or not.

I can do it by carefully using adapter trimming software and discarding a higher proportion of...
Forum: Bioinformatics 01-07-2013, 09:03 PM
Replies: 4
Views: 1,323
Posted By jvanleuven
The attached image is from illumina's "Data...

The attached image is from illumina's "Data Processing of Nextera Mate Pair Reads"

I'm not sure how to tell the difference between templates (a) and (e) without a reference.

I can process...
Forum: Bioinformatics 01-07-2013, 01:48 PM
Replies: 4
Views: 1,323
Posted By jvanleuven
Nextera data analysis recomendations

Hello,

Can anyone recomend software for processing Nextera 100bp PE data.

I could take it through a series of adapter trimming steps, but it seems like there should be a tool that looks for...
Forum: Bioinformatics 05-14-2012, 06:53 AM
Replies: 4
Views: 1,137
Posted By jvanleuven
Thank you yifangt. Hopefully this will get me...

Thank you yifangt. Hopefully this will get me started on the right path.
Forum: Bioinformatics 05-12-2012, 04:51 AM
Replies: 4
Views: 1,137
Posted By jvanleuven
Yes, three categorical independent variables. The...

Yes, three categorical independent variables. The first has 5 possible values, the second has 208 possible values, the third 164 possible values(summary(data) in R).

The same sample was treated in...
Forum: Bioinformatics 05-11-2012, 12:47 PM
Replies: 4
Views: 1,137
Posted By jvanleuven
Simple stats question

Hi all,

I have a pretty simple question on data anaysis, but I'm getting a bit lost in finding the correct statistical tests to run. The data looks like this:

Organism: Gene: Type: ...
Forum: Bioinformatics 12-07-2011, 08:59 PM
Replies: 18
Views: 5,669
Posted By jvanleuven
I will remove the GC bin in my future assemblies,...

I will remove the GC bin in my future assemblies, thank you for the input. While I do not have to worry about accidental cocultures (none of the bacteria I work with are culturable), I do sometimes...
Forum: Bioinformatics 12-07-2011, 08:34 PM
Replies: 18
Views: 5,669
Posted By jvanleuven
I do inclusive searches. First take all contigs...

I do inclusive searches. First take all contigs with similar coverage, then add all contigs with close GC, then add contigs that hit by blast, ect.

Although I am also new at this and still...
Forum: Bioinformatics 12-07-2011, 06:25 AM
Replies: 18
Views: 5,669
Posted By jvanleuven
How do you calculate the 30MB? In every assembly...

How do you calculate the 30MB? In every assembly you could have excess contigs that you don't want to use. If the genome sequence is similar to an already published genome, you can use nucmer or...
Forum: Bioinformatics 11-08-2011, 11:44 AM
Replies: 23
Views: 3,504
Posted By jvanleuven
Yeah, but a lot of my contigs look like this; ...

Yeah, but a lot of my contigs look like this;


NODE_8445_length_3509_cov_38.863495
ATGGGATTGGAATACAAGAAGTTACTTCAAATATATAACATGTCGAACAACAAACATGGA...
Forum: Bioinformatics 11-08-2011, 09:14 AM
Replies: 23
Views: 3,504
Posted By jvanleuven
yeah, i think my reads are sufficiently filtered....

yeah, i think my reads are sufficiently filtered. I think my problem may be a result of such widely varying coverages, or maybe variance in my insert size, or possibly lots of repeats? both genomes...
Forum: Bioinformatics 11-08-2011, 08:49 AM
Replies: 23
Views: 3,504
Posted By jvanleuven
Thanks for all the help. Still not sure about how...

Thanks for all the help. Still not sure about how to fix the N gaps created by scaffolding. I am thinking about using Cap3 to try and cover the gaps with contigs created from a single read assembly...
Forum: Bioinformatics 11-04-2011, 04:06 PM
Replies: 23
Views: 3,504
Posted By jvanleuven
Not sure if that is good enough filtering, this...

Not sure if that is good enough filtering, this is the first time i've tried it.

I think it is pretty good. The first few bases and the last few bases have average qualities around 34, the rest...
Forum: Bioinformatics 11-04-2011, 12:42 PM
Replies: 23
Views: 3,504
Posted By jvanleuven
well, there are probably at least two genomes in...

well, there are probably at least two genomes in there and lots of contaminating host DNA. One genome is pretty easy because it has >95% sequence identity to an annotated genome. The other is more of...
Forum: Bioinformatics 11-04-2011, 12:31 PM
Replies: 23
Views: 3,504
Posted By jvanleuven
okay, thanks. I'll read the papers carefully. ...

okay, thanks. I'll read the papers carefully.

I understand that optimal assembly occurs around 50X.

What I'm not entirely clear on yet is the effects of having scaffolding on or off. With...
Forum: Bioinformatics 11-04-2011, 11:40 AM
Replies: 23
Views: 3,504
Posted By jvanleuven
sorry, I meant to ask why the contigs are so...

sorry, I meant to ask why the contigs are so small. 8000bp is not even close to the size of the genome. 400X coverage implies that there is sufficient data.

jt
Forum: Bioinformatics 11-04-2011, 11:10 AM
Replies: 23
Views: 3,504
Posted By jvanleuven
one of the genomes is at 400X the other is near...

one of the genomes is at 400X the other is near 150X I think. When I assemble with exp_cov 400 and cut_off 50, it increases the contig size to ~8000bp.

Why wont velvet put these contigs together...
Forum: Bioinformatics 11-04-2011, 10:08 AM
Replies: 23
Views: 3,504
Posted By jvanleuven
i tried optimizer, but it seems to like low...

i tried optimizer, but it seems to like low coverage. I have not tried it with specifying my expected coverage.
Forum: Bioinformatics 11-04-2011, 09:55 AM
Replies: 23
Views: 3,504
Posted By jvanleuven
thanks for the helpful suggestions, i really...

thanks for the helpful suggestions, i really appreciate it.

I tried kmer size 57

then tried keeping everything set to auto

$velvetg output_57/ -scaffolding off -ins_length 250 -exp_cov auto...
Forum: Bioinformatics 11-04-2011, 08:50 AM
Replies: 23
Views: 3,504
Posted By jvanleuven
okay, thanks. when scaffolding is off, I...

okay, thanks.

when scaffolding is off, I dont get large contigs. I guess I'll have to try changing parameters again.
Forum: Bioinformatics 11-04-2011, 07:51 AM
Replies: 23
Views: 3,504
Posted By jvanleuven
First time with Velvet

Hi,

Im new to seqanswers and bioinformatics and need a little help with Velvet. I keep getting large blocks of Ns in my PE assembly. The Ns go away when I do an assembly with just the single...
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