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Forum: Bioinformatics 01-14-2017, 09:49 AM
Replies: 4
Views: 3,548
Posted By dsher
I don't know much about the genomics of different...

I don't know much about the genomics of different E. coli strains but isn't that coverage relatively low? If you just mapped the reads to one or more of the known E. coli genomes, what coverage would...
Forum: Bioinformatics 01-14-2017, 06:03 AM
Replies: 4
Views: 3,548
Posted By dsher
Hi Capricy - no updated ideas yet... How do you...

Hi Capricy - no updated ideas yet... How do you know your Illumina assembly covers only 50% of the genome? What kind of libraries did you use, and what coverage did you get on the assembled parts?...
Forum: Bioinformatics 12-19-2016, 11:38 PM
Replies: 4
Views: 3,548
Posted By dsher
Hybrid assembly with low coverage PacBio libraries

Hi everyone,

We are working on sequencing the genomes of a few bacteria and microalgae. We recently had a PacBio run which provided pretty bad results (only 76 MB of data - ~15x coverage of our...
Forum: Sample Prep / Library Generation 12-19-2016, 11:27 PM
Replies: 0
Views: 1,999
Posted By dsher
Advice on getting good PacBio libraries

Hi everyone,

We are having issues getting good quality PacBio libraries from Bacteria and microalgae. Specifically, we got low yield (76 MB) and low length (5,800 bp) from several libraries run on...
Forum: Bioinformatics 06-30-2015, 01:02 PM
Replies: 2
Views: 2,173
Posted By dsher
Thanks Pat for the reply - I have a couple of...

Thanks Pat for the reply - I have a couple of questions but will post them on the blog you mentioned rather than here. In any case if anyone else is reading this I highly recommend having a look at...
Forum: Bioinformatics 06-28-2015, 11:36 AM
Replies: 2
Views: 2,173
Posted By dsher
Very large distance matrix using MOTHUR

Hello,

We are trying to process a large dataset (~200 samples, each with ~100,000 Illumina 250bp 16S reads) using MOTHUR. We now have reached the stage of making a distance matrix to identify...
Forum: Metagenomics 01-28-2015, 11:38 AM
Replies: 3
Views: 1,867
Posted By dsher
Thanks Brian. Do these difficulties extend also...

Thanks Brian. Do these difficulties extend also to comparing between different versions of the same sequencing technique (e.g. between HiSeq and MySeq or between HiSeq or 454 versions as they...
Forum: Metagenomics 01-27-2015, 12:49 PM
Replies: 3
Views: 1,867
Posted By dsher
Comparing metagenomes produces with different sequencing technologies

Hi all,

I would like to compare the abundance of my gene(s) of interest across many published metagenomes. Typically we would normalize the number of hits to the gene length and number of...
Forum: Bioinformatics 01-27-2015, 12:37 PM
Replies: 1
Views: 1,579
Posted By dsher
Hi It seems to me that it is always better to...

Hi
It seems to me that it is always better to treat each replicate separately, at least at the stage of library preparation and sequencing. Not being able to describe the biological variability is...
Forum: Bioinformatics 06-11-2014, 03:05 AM
Replies: 0
Views: 1,295
Posted By dsher
Comparing RNA-seq libraries with different levels of PCR duplication

Hi all,

We are analyzing a set of RNA-seq libraries and noticed that our libraries have very different levels of PCR duplicates, resulting in very different levels of complexity: some libraries...
Forum: RNA Sequencing 01-14-2014, 11:18 AM
Replies: 2
Views: 1,930
Posted By dsher
How can one identify "real" antisense transcripts in prokaryote genomes?

Hello everyone,

We are using directional RNA-seq (Illumina TruSeq® Stranded mRNA Sample Preparation Low Sample (LS) kit) to look at transcriptomes of marine microbes and have noticed that ~3-6% of...
Forum: Bioinformatics 01-12-2014, 11:28 PM
Replies: 2
Views: 1,973
Posted By dsher
Hi Matt, Try Rockhopper -...

Hi Matt,

Try Rockhopper - http://cs.wellesley.edu/~btjaden/Rockhopper/index.html . We have been using it and it seems quite user friendly. The newest version knows how to deal with stranded...
Forum: Bioinformatics 05-20-2013, 01:48 AM
Replies: 4
Views: 8,116
Posted By dsher
Hi HTH - the same questions was asked there three...

Hi HTH - the same questions was asked there three years ago but the issue has not been solved. Any suggestions?
Daniel
Forum: Bioinformatics 05-20-2013, 12:41 AM
Replies: 4
Views: 8,116
Posted By dsher
Retrieving sequence parts using blastdbcmd

Hi all

I am trying to retrieve nucleotide ranges from a BLAST database using blastdbcmd with the -entry_batch option. According to the user manual, blastdbcmd can work with input ranges (in...
Forum: RNA Sequencing 03-10-2013, 11:13 AM
Replies: 1
Views: 1,495
Posted By dsher
Hello, I saw you posted this thread some time...

Hello,
I saw you posted this thread some time ago... did you get any answers, or have you solved the problem? We have a similar case with a high-density bacterial genome, where overlapping genes...
Forum: Bioinformatics 03-10-2013, 11:11 AM
Replies: 2
Views: 3,011
Posted By dsher
Thanks for the tip - but this does not seem to be...

Thanks for the tip - but this does not seem to be the case. We are using relatively few reads and get FPKM=0 with "OK" and not "HIDATA".

looking at IGV, it seems that in several of these cases...
Forum: Bioinformatics 03-09-2013, 10:57 PM
Replies: 11
Views: 3,404
Posted By dsher
Thanks Dong - I just sent a private email with...

Thanks Dong - I just sent a private email with the data (we will follow up with the results on this thread). Daniel
Forum: Bioinformatics 03-09-2013, 11:55 AM
Replies: 11
Views: 3,404
Posted By dsher
Thanks! What email should I send the dropbox...

Thanks! What email should I send the dropbox invitation to?
Forum: Bioinformatics 03-09-2013, 11:20 AM
Replies: 11
Views: 3,404
Posted By dsher
Hi Dong - we don't have BWA installed anywhere as...

Hi Dong - we don't have BWA installed anywhere as a stand-alone yet. Do you have a standalone BWA installed? If so, if I send you a small file with some sequences and the appropriate genome, is...
Forum: Bioinformatics 03-07-2013, 10:20 AM
Replies: 11
Views: 3,404
Posted By dsher
We might try running it directly but part of the...

We might try running it directly but part of the idea is to implement BWA as part of a workflow in Galaxy (we are poor "wet" biologists trying to survive in a world of millions of reads...).
Forum: Bioinformatics 03-04-2013, 04:44 AM
Replies: 2
Views: 3,011
Posted By dsher
FPKM=0 in cufflinks - but there are reads mapped to these genes!

Hello everyone

We are using BAM to map Illumina reads to a bacterial genome, followed by Cufflinks to get the FPKMs (implemented in Galaxy). We have come across many genes for which we get FPKM=0...
Forum: Bioinformatics 03-02-2013, 11:30 AM
Replies: 11
Views: 3,404
Posted By dsher
Hi Dong, Thanks for your reply. Our reads are...

Hi Dong,
Thanks for your reply. Our reads are 40bp long after QC. When we allow n=1 we get many millions of mapped reads(~90% of the reads map well), and increasing n from 1-5 increases the number...
Forum: Bioinformatics 02-28-2013, 12:52 PM
Replies: 11
Views: 3,404
Posted By dsher
BWA with no mismatches - n=0?

Hello,
We have a sample containing several bacterial species and we want to uniquely map RNA-seq reads to the genomes of each of our organisms to get the expression patterns of each organism...
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