Help with bowtie2 for a beginner (windows)

ruchi1621 · 10-23-2013, 06:38 PM

Hello,
As I am completely new to the field of Next Generation Sequencing and I have absolutely no background in computers, I need your help in figuring out the mistakes that I am doing while conducting sequence alignment. I am using bowtie2. The command that I have entered is:

./bowtie2 -p 8 -x hg19 NA11881.fastq > Experiment1.sam

And the result that I get is:

0 reads
0.00% overall alignment rate

I know I am going wrong somewhere. Please help! Any links to help me solve this problem will be appreciated.

Thank you!

Kennels · 10-23-2013, 06:43 PM

Try specifying '-U' in front of your fastq file

ruchi1621 · 10-23-2013, 06:46 PM

Still the same result.

Kennels · 10-23-2013, 07:01 PM

Try also putting '-q' option to specify it is fastq input.
If that still fails, what is the output from

Code:

head NA11881.fastq

some check questions:

Can you post any errors or warning you are getting?
Do you have all the index files in the same directory?
Do you have 8 cpus on your computer?

ruchi1621 · 10-23-2013, 07:49 PM

I am not getting any output for "head NA11881.fastq"

I am not getting any errors or warnings

I have all the index files in the same directory

yes. I have 8 cpus on my computer

Kennels · 10-23-2013, 07:59 PM

Well there's your problem - your fastq file is empty.
The head command gets the first 10 lines from your file.

what do you get with:

Code:

ls -lh NA11881.fastq

ruchi1621 · 10-23-2013, 08:01 PM

On entering:
ls -lh NA11881.fastq

i get

-rw-r--r-- 1 bansalr students 0 Oct 16 14:59 NA11881.fastq

ruchi1621 · 10-23-2013, 08:05 PM

You are right. The file is empty. Let me transfer it again and re-try aligning it. I will get back to you regarding the success of the same. Thanks for your help!

Kennels · 10-23-2013, 08:06 PM

your file size is zero - between 'students' and 'Oct' .

You need to check where and how your downloaded your file. It should not be empty. Perhaps you can get it again from your source. Redo the above commands once you are sure you have reads to align. good luck.

ruchi1621 · 10-24-2013, 10:18 AM

Hi!
I transferred the downloaded the file again and redid the commands and it worked! Thank you so much for your help!

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
I'm a beginner! Help?	smadbro	Sample Prep / Library Generation	3	11-20-2012 07:25 PM
Bioinformatics on Windows and Windows Cloud	xied75	Bioinformatics	1	11-14-2012 01:31 AM
Running Mac on Windows or Get Windows Laptop	lsbrath	General	23	04-04-2012 08:22 AM
Beginner	dr.m.umer	Epigenetics	1	09-20-2011 04:14 AM
A beginner	gongzhichang	Introductions	0	06-03-2011 01:55 AM

10-23-2013, 06:38 PM	#1
ruchi1621 Junior Member Location: USA Join Date: Oct 2013 Posts: 9	Help with bowtie2 for a beginner (windows) Hello, As I am completely new to the field of Next Generation Sequencing and I have absolutely no background in computers, I need your help in figuring out the mistakes that I am doing while conducting sequence alignment. I am using bowtie2. The command that I have entered is: ./bowtie2 -p 8 -x hg19 NA11881.fastq > Experiment1.sam And the result that I get is: 0 reads 0.00% overall alignment rate I know I am going wrong somewhere. Please help! Any links to help me solve this problem will be appreciated. Thank you!

10-23-2013, 07:01 PM	#4
Kennels Senior Member Location: Sydney Join Date: Feb 2011 Posts: 149	Try also putting '-q' option to specify it is fastq input. If that still fails, what is the output from Code: head NA11881.fastq some check questions: Can you post any errors or warning you are getting? Do you have all the index files in the same directory? Do you have 8 cpus on your computer?

10-23-2013, 07:59 PM	#6
Kennels Senior Member Location: Sydney Join Date: Feb 2011 Posts: 149	Well there's your problem - your fastq file is empty. The head command gets the first 10 lines from your file. what do you get with: Code: ls -lh NA11881.fastq

10-23-2013, 06:43 PM	#2
Kennels Senior Member Location: Sydney Join Date: Feb 2011 Posts: 149	Try specifying '-U' in front of your fastq file

10-23-2013, 06:46 PM	#3
ruchi1621 Junior Member Location: USA Join Date: Oct 2013 Posts: 9	Still the same result.

10-23-2013, 07:49 PM	#5
ruchi1621 Junior Member Location: USA Join Date: Oct 2013 Posts: 9	I am not getting any output for "head NA11881.fastq" I am not getting any errors or warnings I have all the index files in the same directory yes. I have 8 cpus on my computer

10-23-2013, 08:01 PM	#7
ruchi1621 Junior Member Location: USA Join Date: Oct 2013 Posts: 9	On entering: ls -lh NA11881.fastq i get -rw-r--r-- 1 bansalr students 0 Oct 16 14:59 NA11881.fastq

10-23-2013, 08:05 PM	#8
ruchi1621 Junior Member Location: USA Join Date: Oct 2013 Posts: 9	You are right. The file is empty. Let me transfer it again and re-try aligning it. I will get back to you regarding the success of the same. Thanks for your help!

10-23-2013, 08:06 PM	#9
Kennels Senior Member Location: Sydney Join Date: Feb 2011 Posts: 149	your file size is zero - between 'students' and 'Oct' . You need to check where and how your downloaded your file. It should not be empty. Perhaps you can get it again from your source. Redo the above commands once you are sure you have reads to align. good luck.

10-24-2013, 10:18 AM	#10
ruchi1621 Junior Member Location: USA Join Date: Oct 2013 Posts: 9	Hi! I transferred the downloaded the file again and redid the commands and it worked! Thank you so much for your help!