SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-Seq: S-MART, A Software Toolbox to Aid RNA-seq Data Analysis. Newsbot! Literature Watch 0 10-15-2011 04:11 AM
RNA-Seq: GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Newsbot! Literature Watch 0 10-15-2011 04:11 AM
RNA-Seq: RseqFlow: Workflows for RNA-Seq data analysis. Newsbot! Literature Watch 0 07-29-2011 03:00 AM
RNA-Seq: De novo assembly and analysis of RNA-seq data. Newsbot! Literature Watch 0 10-12-2010 04:50 AM
RNA-Seq: RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome. Newsbot! Literature Watch 0 08-07-2010 03:54 AM

Reply
 
Thread Tools
Old 11-05-2011, 02:39 PM   #61
frymor
Senior Member
 
Location: Germany

Join Date: May 2010
Posts: 150
Arrow

Hi,

I was wondering if there is a typo in the script here:
Code:
awk '$3!="*"' untreated1.fa|wc -l
wc -l untreated1.fa
Did you mean to check the sam file? (untreated1.sam)
How can you see in the fastA file how many reads were aligned?

Thanks
frymor is offline   Reply With Quote
Old 03-20-2012, 10:43 AM   #62
yqxiong
Junior Member
 
Location: Florida, USA

Join Date: Nov 2009
Posts: 1
Talking Thanks for the nice tutorial

I was looking for such a tutorial for some time. I got it now. Thanks a lot!
yqxiong is offline   Reply With Quote
Old 03-21-2012, 12:52 AM   #63
caoyh
Junior Member
 
Location: BJ

Join Date: Mar 2012
Posts: 1
Default

Thanks very much.
This is the right tutorial for me..
caoyh is offline   Reply With Quote
Old 03-23-2012, 09:49 AM   #64
himanshu04
Member
 
Location: New York

Join Date: Mar 2012
Posts: 35
Default

Hey everyone,
I am new to NGS and I was trying the DE analysis of Di Arabidopsis pathogen data as mentioned in the tutorial. I followed every step and in the end I got the count of significant genes to be 169. I wanted to know how do I get the file that describes all the significant genes?. Any help will be much appreciated since I am still in the learning phase.
Thanks in advance,
Himanshu.
himanshu04 is offline   Reply With Quote
Old 03-29-2012, 06:38 AM   #65
lilletine
Junior Member
 
Location: Bergen, Norway

Join Date: Jan 2012
Posts: 7
Smile

Thank you for the very nice tutorial, and also for guiding me to the 'how-to-wiki'!!
lilletine is offline   Reply With Quote
Old 04-20-2012, 02:41 PM   #66
rna_follower
Junior Member
 
Location: Canada

Join Date: Apr 2012
Posts: 2
Default

Hi,

I am trying to install miRanalyzer stand alone version. I have built the database and managed to download all required tools and packages. When I tried to run it with the test data provided, I get this message: "Failed to load Main-Class manifest attribute from miRanalyzer.jar
". Just wondering what I am doing wrong
rna_follower is offline   Reply With Quote
Old 07-17-2012, 01:27 AM   #67
Ajayi Oyeyemi
Member
 
Location: Abeokuta

Join Date: Jul 2012
Posts: 30
Default the seven fasta files by Li et al., 2008

Can anyone help me in giving a link on the seven fasta files by Li et al 2008 used in the RNA-seq tutorial posted just of recent?
Ajayi Oyeyemi is offline   Reply With Quote
Old 08-16-2012, 12:13 AM   #68
Gateway
Junior Member
 
Location: Sg

Join Date: Jul 2012
Posts: 1
Default

Hi

When making Exon Junction libraries, you suggest to use Make Splice Junction Fasta (USeq software package). I've read on their web page that it's depreciated and Make Transcriptome (USeq's package as well) should be used instead.

Make Transcriptome gives 2 outputs; transcripts and splices. I guess I shall use only splices file in further step(s). Am I right?
Gateway is offline   Reply With Quote
Old 12-11-2012, 04:07 PM   #69
Ajayi Oyeyemi
Member
 
Location: Abeokuta

Join Date: Jul 2012
Posts: 30
Default

Hi,
I'm very new to RNA sequencing analysis and I've been using Trapnell et al., 2012 protocol as a guide. I've succesfully downloaded the softwares including the fruitfly genome in "my_rna_seq" directory as advised and I try as much as possible to move files extracted in the Downloads to this directory so that I can have everything in the above mentioned directory.
The challenge came when I wanted to align my RNA-seq reads to the reference genome. After the first command, all I got was an error indicating that "Could not find Bowtie index files C1_R1_1.fq.*" I'm faced with this error monster and I just need a clue to find this monster.
I have the following files in my folder:
bowtie-0.12.8
bowtie-0.12.8-linux-x86_64.zip
C1_R1_thout
C1_R1_thout--library-type=fr-firststrand genome
d_melanogaster_fb5_22.1.ebwt
d_melanogaster_fb5_22.2.ebwt
d_melanogaster_fb5_22.3.ebwt
d_melanogaster_fb5_22.4.ebwt
d_melanogaster_fb5_22.ebwt.zip
d_melanogaster_fb5_22.rev.1.ebwt
d_melanogaster_fb5_22.rev.2.ebwt
Drosophila_melanogaster
Drosophila_melanogaster_Ensembl_BDGP5.25.tar.gz
Ensem
genes.gtf
genome.*.
GSE32038_simulated_fastq_files.tar.gz
GSM794483_C1_R1_1.fq.gz
GSM794483_C1_R1_2.fq.gz
GSM794484_C1_R2_1.fq.gz
GSM794484_C1_R2_2.fq.gz
GSM794485_C1_R3_1.fq.gz
GSM794485_C1_R3_2.fq.gz
GSM794486_C2_R1_1.fq.gz
GSM794486_C2_R1_2.fq.gz
GSM794487_C2_R2_1.fq.gz
GSM794487_C2_R2_2.fq.gz
GSM794488_C2_R3_1.fq.gz
GSM794488_C2_R3_2.fq.gz
make_d_melanogaster_fb5_22.sh
README.txt
tophat_out

and I used this command:
tophat -p 8 -G genes.gtf -o C1_R1_thout--library-type=fr-firststrand\ genome C1_R1_1.fq C1_R1_2.fq

Thanks.
Ajayi Oyeyemi is offline   Reply With Quote
Old 12-12-2012, 10:04 PM   #70
hanifk
Member
 
Location: China

Join Date: Oct 2010
Posts: 18
Default

I am not familiar with tophat, but I have been using bowtie.

Before the mapping process of bowtie, it should index the reference genome using the command such as:
bowtie-build hg19.fasta hg19
then six files (hg19.1.ebwt, hg19.2.ebwt, hg19.3.ebwt, hg19.4.ebwt, hg19.rev.1.ebwt, and hg19.rev.2.ebwt) will be generated.

During the process of mapping, bowtie searched the short reads(usually *.fq) again those six indexed files.

I think the index process and mapping process have been automated by tophat.

In your question, it reports "Couldn't find index files C1_R1_1.fq.* ".
I guess the reference genome should be d_melanogaster_fb5_22

did you forget to specify the reference genome in your command?
tophat -p 8 -G genes.gtf -o C1_R1_thout--library-type=fr-firststrand\ genome C1_R1_1.fq C1_R1_2.fq

hope can help you



Quote:
Originally Posted by Ajayi Oyeyemi View Post
Hi,
I'm very new to RNA sequencing analysis and I've been using Trapnell et al., 2012 protocol as a guide. I've succesfully downloaded the softwares including the fruitfly genome in "my_rna_seq" directory as advised and I try as much as possible to move files extracted in the Downloads to this directory so that I can have everything in the above mentioned directory.
The challenge came when I wanted to align my RNA-seq reads to the reference genome. After the first command, all I got was an error indicating that "Could not find Bowtie index files C1_R1_1.fq.*" I'm faced with this error monster and I just need a clue to find this monster.
I have the following files in my folder:
bowtie-0.12.8
bowtie-0.12.8-linux-x86_64.zip
C1_R1_thout
C1_R1_thout--library-type=fr-firststrand genome
d_melanogaster_fb5_22.1.ebwt
d_melanogaster_fb5_22.2.ebwt
d_melanogaster_fb5_22.3.ebwt
d_melanogaster_fb5_22.4.ebwt
d_melanogaster_fb5_22.ebwt.zip
d_melanogaster_fb5_22.rev.1.ebwt
d_melanogaster_fb5_22.rev.2.ebwt
Drosophila_melanogaster
Drosophila_melanogaster_Ensembl_BDGP5.25.tar.gz
Ensem
genes.gtf
genome.*.
GSE32038_simulated_fastq_files.tar.gz
GSM794483_C1_R1_1.fq.gz
GSM794483_C1_R1_2.fq.gz
GSM794484_C1_R2_1.fq.gz
GSM794484_C1_R2_2.fq.gz
GSM794485_C1_R3_1.fq.gz
GSM794485_C1_R3_2.fq.gz
GSM794486_C2_R1_1.fq.gz
GSM794486_C2_R1_2.fq.gz
GSM794487_C2_R2_1.fq.gz
GSM794487_C2_R2_2.fq.gz
GSM794488_C2_R3_1.fq.gz
GSM794488_C2_R3_2.fq.gz
make_d_melanogaster_fb5_22.sh
README.txt
tophat_out

and I used this command:
tophat -p 8 -G genes.gtf -o C1_R1_thout--library-type=fr-firststrand\ genome C1_R1_1.fq C1_R1_2.fq

Thanks.
hanifk is offline   Reply With Quote
Old 07-23-2013, 12:57 AM   #71
BobbyKing
Junior Member
 
Location: Cranfield

Join Date: Jul 2013
Posts: 2
Default

I have put together a tutorial website with four core tutorials on it, RNA-Seq, ChIP-Seq, Genome assembly, and SNP calling that may be of use to you.

This website was created to share bioinformatics tutorials and create a dynamic learning environment that does not become dated, PDF contributions welcome and there are four core tutorials available. We would be interested to get some feedback.

http://elvis.ccc.cranfield.ac.uk/CUB...gin-page.xhtml
BobbyKing is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:43 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO