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Search: Posts Made By: Alun3.1
Forum: Bioinformatics 04-10-2015, 10:48 PM
Replies: 2
Views: 2,077
Posted By Alun3.1
Thanks Brian ! It makes more sense...

Thanks Brian !


It makes more sense indeed.
However, I also just tried samtools view and got the same number of sequences as bowtie calculatedsamtools -c -F 4 <input.sam>
The trick is that I...
Forum: Bioinformatics 04-10-2015, 09:52 PM
Replies: 2
Views: 2,077
Posted By Alun3.1
Basic question mapping read/contigs (Bowtie2)

Hi,

I am learning bioinformatics and have a basic question about bowtie2.

I got 2 different sets of single-end sequencing reads:
- set #1: 10,000,000 reads
- set #2: 12,000,000 reads
...
Forum: Bioinformatics 03-11-2015, 12:08 AM
Replies: 2
Views: 1,816
Posted By Alun3.1
Assembly quality RSEM-EVAL failing

Hi,

I am trying to run rsem-eval from the Detonate 1.8.1 package to assess the quality of a transcriptome assembly.

I use the following command (on a cluster with ncpus=8:mem=20G):...
Forum: Bioinformatics 02-26-2015, 05:08 PM
Replies: 4
Views: 1,069
Posted By Alun3.1
Got it. Thanks westerman !

Got it. Thanks westerman !
Forum: Bioinformatics 02-24-2015, 07:50 PM
Replies: 4
Views: 1,069
Posted By Alun3.1
Program for aligning particular set of reads to an entire NGS dataset

Hi,

I have about 100 cDNA sequences (let's call them "ref.") for which I would like to know how many reads from the original Illumina dataset (10 millions of reads; let's call them "reads") align...
Forum: RNA Sequencing 02-24-2015, 07:13 PM
Replies: 9
Views: 2,967
Posted By Alun3.1
Thanks guys for your replies !

Thanks guys for your replies !
Forum: RNA Sequencing 02-23-2015, 04:48 PM
Replies: 9
Views: 2,967
Posted By Alun3.1
Thanks sarvidsson ! So I assume it...

Thanks sarvidsson !



So I assume it also depends on the species you study, the complexity of the transcriptome, the length of the reads (and the cost of the sequencing).
What about if you only...
Forum: RNA Sequencing 02-22-2015, 09:24 PM
Replies: 9
Views: 2,967
Posted By Alun3.1
Is it possible to estimate mRNA-seq depth/coverage just with genome size?

Hi,

Being a newbie in NGS, I have a very basic question.

I sequenced tissue mRNAs using a paired-end strategy.
Is it possible to calculate the depth of an overall mRNA-seq experiment when no...
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