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Forum: Oxford Nanopore 08-11-2017, 09:41 AM
Replies: 7
Views: 4,487
Posted By JonB
That's also the case for me. I work on an algae...

That's also the case for me. I work on an algae and I struggle to get a lot of DNA due to sub-optimal cultures. But the DNA I have is of really high quality though.

Thanks for all the suggestions....
Forum: Oxford Nanopore 08-10-2017, 11:32 PM
Replies: 7
Views: 4,487
Posted By JonB
Thanks! Yes, I was not sure about which order...

Thanks!
Yes, I was not sure about which order to do things (assembly and correction). But your suggestion is very helpful.
Forum: Oxford Nanopore 08-10-2017, 10:48 PM
Replies: 7
Views: 4,487
Posted By JonB
Thanks for the manuscript! I'm not exactly sure...

Thanks for the manuscript!
I'm not exactly sure about the Illumina coverage at the moment, but it's very high at least. Mostly I was concerned about using only 1D because of the error rate, but I...
Forum: Oxford Nanopore 08-08-2017, 11:38 PM
Replies: 7
Views: 4,487
Posted By JonB
Assembly using Illumina + Nanopore 1D reads?

Hi,

I am trying to assemble a eukaryotic genome of about 300MB. I have Illumina data, and I am thinking of trying out the MinION Basic Starter Pack to use for scaffolding. But it produces only 1D...
Forum: Sample Prep / Library Generation 03-31-2016, 01:42 AM
Replies: 0
Views: 879
Posted By JonB
BROAD cDNA-preparation - random primed or oligo-dT?

Hi,

I am looking into the RNA-Seq data from BROAD institute (SRA: SRX099331) and wonder whether the cDNA was created by random priming or with oligo-dT. Anyone know? I tried to send them an email,...
Forum: General 02-18-2016, 09:30 AM
Replies: 1
Views: 1,079
Posted By JonB
Submit Illumina data to Dryad, SRA, ENA...?

Where do people prefer to submit their NGS/Illumina data? I like Dryad because the data is linked to the publication. But I don't know how easy it is to find and access NGS-data from Dryad. And with...
Forum: RNA Sequencing 02-15-2016, 03:11 AM
Replies: 3
Views: 1,785
Posted By JonB
Thanks! No we didn't deplete rRNAs, so...

Thanks!
No we didn't deplete rRNAs, so definitely rRNAs represent a major fraction of the reads. But do you think this can explain the differences in mapping rate between tap+ and tap-? And should...
Forum: RNA Sequencing 02-15-2016, 12:58 AM
Replies: 3
Views: 1,785
Posted By JonB
Low mapping rate of TSS-data (5'-seq)

Hi,

We have performed transcription start site sequencing (TSS, 5'-sequencing) using TAP treatment (tap+ and tap- of totalRNA) and Illumina 100bp SE sequencing. I have quality trimmed the reads...
Forum: Bioinformatics 12-11-2015, 12:53 AM
Replies: 5
Views: 2,416
Posted By JonB
I should have mentioned that I do have stranded...

I should have mentioned that I do have stranded sequencing. So I guess I will map the R2 reads separately.
Thanks!
Forum: Bioinformatics 12-10-2015, 11:28 PM
Replies: 5
Views: 2,416
Posted By JonB
The paired reads are sequenced like this ...

The paired reads are sequenced like this
R1------> <------R2
and I guess tophat takes this into account when it is fed paired reads. But when it only gets the R2 reads as single end, without...
Forum: Bioinformatics 12-10-2015, 02:03 AM
Replies: 2
Views: 2,102
Posted By JonB
Thanks! I think also Tophat can take a mix of...

Thanks! I think also Tophat can take a mix of paire-end and single-end reads.
Forum: Bioinformatics 12-10-2015, 01:57 AM
Replies: 5
Views: 2,416
Posted By JonB
Mixing paired-end and single-end reads in Tophat: Do I have to reverse the SE-reads f

This is a cross-post from the Tuxedo Google group: https://groups.google.com/forum/#!topic/tuxedo-tools-users/BtI3_fp_n-o

And a follow-up from a previous post...
Forum: Bioinformatics 12-09-2015, 09:33 AM
Replies: 2
Views: 2,102
Posted By JonB
Mapping paired-end reads, include also the SE-reads after trimming?

Hi,

I have trimmed paired-end reads with Trimmomatic, and some reads are therefore left as only single-end (one pair filtered out entirely). I am using tophat2 to map against a reference genome...
Forum: Bioinformatics 12-07-2015, 11:05 PM
Replies: 2
Views: 1,738
Posted By JonB
Hi, No hardware problems. It was simply me who...

Hi,
No hardware problems. It was simply me who made a silly mistake. Don't remember exactly, but I think it was a problem with some of the input files.
Forum: Bioinformatics 05-28-2015, 06:15 AM
Replies: 0
Views: 2,303
Posted By JonB
Difference between Cufflinks coverage and HTSeq-count

Hi,

I am struggling to understand the coverage value (not fpkm) produced by cufflinks. In my case it seems to be much lower than the values produced by htseq-count. I thought the cufflinks...
Forum: Bioinformatics 05-27-2015, 07:17 AM
Replies: 0
Views: 1,172
Posted By JonB
Does anyone know how cufflinks counts stranded data?

Hi,

I'm trying to make sense of the fpkm/coverage values produced by cufflinks. I have mapped paired-end stranded illumina data (fr-firststrand type).

But the coverage values are not similar to...
Forum: Bioinformatics 04-28-2015, 07:34 AM
Replies: 2
Views: 1,738
Posted By JonB
GMAP problems: stopping at "Finished checking compiler assumptions"

Edit:
Never mind. It was a simple database error. Fixed it, but don't know how to delete post...

I am trying to map around 300 cDNA sequences to a genome using GMAP. I encountered some problems...
Forum: Bioinformatics 07-12-2014, 09:40 AM
Replies: 1
Views: 5,555
Posted By JonB
Extract gene sequences from gff3 file and reference fasta

Hi,

I have a gff3 file and I want to extract the gene sequences (not including introns). Several genes have many isoforms, but I want only the gene sequence (i.e. all the exons spliced). Anyone...
Forum: Bioinformatics 07-11-2014, 01:20 AM
Replies: 6
Views: 1,368
Posted By JonB
Dear Mike, Sorry for asking novice...

Dear Mike,

Sorry for asking novice questions.
I have only one variable to my design (condition) that includes all the different stages as well as the non-reproductive stages (which I want to use...
Forum: Bioinformatics 07-11-2014, 12:40 AM
Replies: 6
Views: 1,368
Posted By JonB
Thanks! Jon

Thanks!

Jon
Forum: Bioinformatics 07-10-2014, 08:27 AM
Replies: 6
Views: 1,368
Posted By JonB
Need advice on analysing RNA-seq time series

Hi everyone,

I have performed RNA-seq from different stages of embryogenesis. Some stages have two, three or four replicates, while some have none. I want to identify a set of genes that I can say...
Forum: Bioinformatics 06-09-2014, 01:50 PM
Replies: 2
Views: 4,144
Posted By JonB
DEseq2: can filtering low count genes reduce the number of DE genes?

Hi,

I tried to filter out genes with a count less than 2.0, and it seems that the lowest padj value for these genes is 1.350968e-44, and that removing these genes reduces the number of DE genes....
Forum: Bioinformatics 06-09-2014, 01:00 PM
Replies: 4
Views: 3,500
Posted By JonB
Ah, I see. That makes sense. Thanks!

Ah, I see. That makes sense. Thanks!
Forum: Bioinformatics 06-09-2014, 12:38 PM
Replies: 4
Views: 3,500
Posted By JonB
Here's the code I used: library("DESeq2") ...

Here's the code I used:

library("DESeq2")

#Set the directory where the HTSeq count files are located
directory = "/Users/jonbra/Desktop/Gene_count_files/"

#Catch the files with the pattern...
Forum: Bioinformatics 06-08-2014, 02:09 PM
Replies: 10
Views: 3,320
Posted By JonB
Thanks guys, I actually didn't know there was a...

Thanks guys,
I actually didn't know there was a DESeq2. I will check it out asap
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