22 results in 0.0037 seconds.
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Find gene duplications in a draft genome assembly
Hi everyone, I have recently assembly a draft genome. I consider it has an acceptable quality based on the assessment I made and my biological goals.... -
Transcriptome assembly: Low GC, short contigs, low read alignment
Hi,
Sorry if this is a repeat. I posted earlier but now can't find it under the posts/threads listed under my username...
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cufflinks: input alignment from hisat2
Hi all,
I read on Cufflinks man page that input bam file must be sorted this way:
sort -k 3,3 -k 4,4n hits.sam > hits.sam.sorted... -
Webinar 6/22: Speed, Accuracy and Capacity for Your NGS Analysis Projects
Join us for a webinar tomorrow, June 22 at 12 pm EDT/9 am PDT.
DNASTAR NGS Senior Applications Manager, Matt Keyser and VP of Sales, Dr.... -
Webinar: RNA-Seq for Non-Model Organisms
Join us for a webinar on Wednesday, April 27 at 12:00 PM EDT (GMT -4:00).
DNASTAR’s Matthew Keyser will give a live software demonstration... -
Webinar: De Novo Transcriptome Assembly, Auto-Annotation and RNA-Seq For Any Organism
Join DNASTAR for a webinar on Wednesday, March 9 at 1:00 PM EST (GMT -5:00), where we will present our new software workflow for de novo transcriptome... -
stringtie parameters
Hi,
I have been trying to use Stringtie for transcriptome re-assembly, based on a reference gtf file.
Here is how I ran it:
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optimizing transcriptome assembly
Hi All,
I wanted to make sure people have seen the new Oyster River Protocol for transcriptome assembly. In brief, it’s an evidence... -
Chimic contigs detection; fusioncatcher; UCHIME
Hello
I de novo assembled a transcriptome. I would like to detect chimeras in it. IS there any other software, which may help my?
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How come that the Trinity assembler seems to work on a computer with low memory
Hi Dear All
I have a dataset (about 60m reads paired or 120m together~ 14.5Gb each file). at the first I run trinity (latest version) ... -
Oases python script can't find Velvet
Aloha,
So, I'm trying to run Oases to create a de novo transcriptome. I have the paired-end reads file ready to go, and the newest versions... -
how to minimize transcripts while de novo assembly transcriptome
Hi all,
I am using Trinity for de novo assembly of mRNA from Illumina Hiseq2000, 100bp pair ends. We get more than 11M clean reads of... -
Can Cufflinks handle bam files from outside?
By bam from outside, I mean the alignment made not by TopHat.
Here in http://www.biostars.org/p/10278/ (2.4 years ago), Leszek said TopHat does... -
SOAP denov "missing reads"
Hi there,
my question is about denovo assembly using SOAP denovo-trans. I have data from a MiSeq, 20 Mio paired end reads, 250bp each,... -
SOAPdenovo-Trans and IDBA-Tran for transcriptome assembly
I was wondering if any users have experience using SOAPdenovo-Trans and/or IDBA-Tran for transcriptome assembly.
I have had reasonable...
