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Forum: RNA Sequencing 08-06-2018, 08:00 PM
Replies: 0
Views: 1,861
Posted By Name_less_
Script for FPKM with Deseq2 - help

Hello to all.
I'm new in R, but I'm working with RNA-seq data for a work in a course.
Specifically, I have a count matrix similar to that:

gene sample1 sample2 sample3 sample4 gene_length(nt)...
Forum: RNA Sequencing 05-22-2018, 08:13 AM
Replies: 1
Views: 1,538
Posted By Name_less_
Questions about small RNA-seq (single-end and strand-specific)

Hello everyone!
I'm new analyzing transcriptomic.
I have small RNA-seq data, single-end from Rat.
Initially, I mapped the data with Bowtie with next command:

bowtie -p 50 --mm -n 0 --best...
Forum: Epigenetics 05-22-2018, 07:37 AM
Replies: 2
Views: 2,760
Posted By Name_less_
Thank you! So I will merge the fastq files. ...

Thank you! So I will merge the fastq files.
Referent to point 2:
I have 9 folders, 2 for each replicate (WT1, WT2, C1, C2, V1, V2) and other three (WTIN, CIN, VIN). I talked with my friend and he...
Forum: Epigenetics 05-15-2018, 12:53 PM
Replies: 2
Views: 2,760
Posted By Name_less_
Chip-seq data questions

Hello
I need work with Chip-seq of 3 conditions (WT, C and V). Itís single-end.
When I saw the data, questions born:

1. Each sample has duplicate, but each duplicate has 4 fastq files...
Forum: Bioinformatics 11-06-2015, 10:29 AM
Replies: 1
Views: 683
Posted By Name_less_
Pair-end bowtie questions

Hello everyone!!
I'm new in the work with sequencing, more specific Chip-seq data set. I have pair-end data and mapped it with bowtie2. I have read the SAM format specifications but don't understand...
Forum: RNA Sequencing 10-27-2014, 07:03 AM
Replies: 4
Views: 1,372
Posted By Name_less_
Hi Finally I used DEseq2 and I could get what I...

Hi
Finally I used DEseq2 and I could get what I expected. Thanks for all and greetings !!
Forum: Bioinformatics 10-27-2014, 06:48 AM
Replies: 6
Views: 1,237
Posted By Name_less_
Sorry for the late but I was full work. Thanks...

Sorry for the late but I was full work.
Thanks for all. That was the solution. Thanks!!! Now I can create the graphics needed.
THANKS!! jeje
Greetings!
Forum: Bioinformatics 10-09-2014, 05:39 PM
Replies: 6
Views: 1,237
Posted By Name_less_
This is what the csScatter prints in my screen: ...

This is what the csScatter prints in my screen:

> csDensity(genes(cuff_data))
Mensajes de aviso perdidos
1: Removed 6 rows containing non-finite values (stat_density).
2: Removed 3 rows...
Forum: RNA Sequencing 10-09-2014, 09:43 AM
Replies: 4
Views: 1,372
Posted By Name_less_
The table looks as expected, but I will try of...

The table looks as expected, but I will try of use DESeq2. However, still I can not solve this problem in DESEQ.
Forum: Bioinformatics 10-09-2014, 09:33 AM
Replies: 6
Views: 1,237
Posted By Name_less_
No, I have similar error with csVolcano. I...

No, I have similar error with csVolcano. I followed the steps of the TOPHAT paper (Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, nature...
Forum: Bioinformatics 10-09-2014, 07:20 AM
Replies: 6
Views: 1,237
Posted By Name_less_
Help with cummeRbund

Hello
I am new in R, but I am work with cummeRbund.
I followed the next steps:

> library(cummeRbund)
> cuff_data < - readCufflinks("diff_out")
> csDensity(genes(cuff_data))
> ...
Forum: RNA Sequencing 10-09-2014, 06:14 AM
Replies: 4
Views: 1,372
Posted By Name_less_
Help with DESeq please

Hello everyone
I am new in the use of DESeq and I have problems for obtain Diferencial Expression of an Output of EDGE-Pro.
In R, I followed the steps on this page:
...
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