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Forum: RNA Sequencing 07-05-2018, 10:16 AM
Replies: 10
Views: 13,711
Posted By caiosuz
Low percentage of mapped reads

I used STAR to align reads of 8 RNASeq libraries against the reference genome of the plant citrus sinensis and I got mapping results that I consider very low, once I've seen many published works with...
Forum: Bioinformatics 08-19-2016, 04:20 AM
Replies: 3
Views: 958
Posted By caiosuz
Thanks a lot, offspring. I will re-run my...

Thanks a lot, offspring.
I will re-run my mapping with this new issue!
=D
Forum: Bioinformatics 08-19-2016, 03:47 AM
Replies: 3
Views: 958
Posted By caiosuz
Unhappy Crazy unmapped reads

I don't know if I am understanding the correct meaning of the reads index in sam files.

This information is present in the Flags description:

'Next, we have the cases when only one read in a...
Forum: Bioinformatics 08-18-2016, 05:30 AM
Replies: 14
Views: 15,670
Posted By caiosuz
Crazy TopHat unmapped reads

Did anyone have the same problem with these unmapped reads?
Forum: Bioinformatics 08-17-2016, 11:50 AM
Replies: 14
Views: 15,670
Posted By caiosuz
What's going on here?

I don't know if I am understanding the correct meaning of the reads index in sam files.

This information is present in the Flags description:

'Next, we have the cases when only one read in a...
Forum: RNA Sequencing 06-03-2016, 07:23 AM
Replies: 1
Views: 1,590
Posted By caiosuz
Velvet usage

Hi everyone!

I'm trying to use velvet to work with unmapped_reads of a rna-seq experiment, to make a kind of quantification of the contaminants of my sample.

I was reading this quick guide...
Forum: RNA Sequencing 02-15-2016, 09:00 AM
Replies: 14
Views: 1,957
Posted By caiosuz
I was thinking about a way to run tophat again...

I was thinking about a way to run tophat again with my unmmapped reads.
Can anyone give suggestions of changing of values of parameters to loose the stringency of the analyse without losing mapping...
Forum: Bioinformatics 02-15-2016, 08:46 AM
Replies: 3
Views: 2,514
Posted By caiosuz
Thanks for the tip chuckcode. It worked...

Thanks for the tip chuckcode.
It worked perfectly!
Forum: RNA Sequencing 01-06-2016, 09:30 AM
Replies: 14
Views: 1,957
Posted By caiosuz
Wink TopHat2 - Low percentage of mapped reads

Hi, everyone!
I'm worried about my mapping results with TopHat2.
I'm working with five sets of reads and these are the mapping results:

S1 - 65.8 %
S2 - 29.6 %
S3 - 80.3 %
S4 - 15.4 %
S5 -...
Forum: Bioinformatics 12-05-2015, 04:31 PM
Replies: 2
Views: 1,240
Posted By caiosuz
Question Installing R in ubuntu

Hi everyone!
I need to install R for using the cummeRbund package.
When I try to install it through apt-get the R version installed is too old for some dependencies of cummeRbund.
Even after I...
Forum: RNA Sequencing 12-03-2015, 10:00 AM
Replies: 1
Views: 803
Posted By caiosuz
Post Running TopHat

Hi, fellows!
I would like to ask for your help concerning to the execution of TopHat.
I am working with reads from mRNA generated by a MiSeq machine.
Although this software had been developed for...
Forum: Bioinformatics 12-03-2015, 08:44 AM
Replies: 3
Views: 3,037
Posted By caiosuz
Thanks a lot, I had the same problem and the...

Thanks a lot, I had the same problem and the solution worked for me either! =)
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