Entering edit mode
9.5 years ago
bioinfo_student
•
0
Hi,
I am a new student in bioinformatics.
I am trying to start using Bowtie2 to map libraries to a particular genome to observe unique tags. Can someone help me with this? If so I can elaborate a little on what I am specifically looking at.
Hope someone will reach out to me :D
Ash
You need to align those reads against the reference genome using bowtie2 and then check is they are aligned uniquely. Check this post: Best Way To Get Truly Unique Reads In Bowtie/Sam?
Thank you.
I need to convert .srt files to fastQ right?
:) Sorry if questions sound silly, Thanks for helping!
Never heard about .srt file. Did you mean .sra ?
First you need to convert whatever format you have to fastq or fasta file format. Then you will have to index your reference genome using bowtie build index and then align fastq or fasta file against the genome. You will get the sam/bam file as output. You can also then process sam/bam file to extract unique reads.
Thanks a lot! It's clear now! :D
convert sra file by sratoolkit (install if you haven't) by
have you made bowtie index?
The purpose here is for you to reach out to others. "If so I can elaborate a little on what I am specifically looking at." Specificity in asking your questions is huge, you should include it first, not as an afterthought. Even if you can help inform others with your question, this is helpful. For instance, do you have some reason to suspect that analysis of CAGE libraries is any different than analysis of any general library? (I've never analyzed CAGE data, so I don't know, but I've analyzed tons of other data). Otherwise the answer to your question could be seen in the first part of the bowtie manual, perhaps something as simple as: bowtie -m 1.
No I just meant I was starting to use bowtie... I just randomly try some problems or exercise. I recently read a paper ,so I intended to try it, so I was just clarifying.
The reason Why I didn't elaborate so much at first, I thought it would be too much. Like this, since the answer is simple, not much detail needed, But if to answer anyone needed more specificity I could have discussed further on the exercise I am with. I am a mere beginner and I am using the tutorial. Was just expecting a little additional support.