hanshart Member

Location: Germany

Join Date: Nov 2011 Posts: 27

Quote: vishnuamaram Originally Posted by ...

Q) i am struck to go further with analysis as i am not sure of how to perform indexing.

--> what does the indexing do exactly. do we need to consider the Chr un... files for indexing.

kindly let me know the downstream analysis steps with clarity.

Will be very thankful to you.

Vishnu.

The indexing itself is not that important for you, it is just an algorithm to store your reference in a nice data structure. Every aligner uses it's own indexing strategy based on the alignment strategy.

What you want to do next is the alignment/mapping of your trimmed reads to a reference. For this you need a program like STAR, TopHat, Bowtie 1/2, BWA, .... So, you have to decide which mapping program to use and which reference. It is up to you and your biological questions, whether you want to include unplaced contigs (chr_Un...,

Code: bowie-build REF_FASTA IDX_FOLDER/IDX_NAME

For every mapping with Bowtie against this reference you have to provide the path to this index, as it is in fact just another representation of your reference FASTA.

Hope this helps Hi Vishnu,The indexing itself is not that important for you, it is just an algorithm to store your reference in a nice data structure. Every aligner uses it's own indexing strategy based on the alignment strategy.What you want to do next is the alignment/mapping of your trimmed reads to a reference. For this you need a program like STAR, TopHat, Bowtie 1/2, BWA, .... So, you have to decide which mapping program to use and which reference. It is up to you and your biological questions, whether you want to include unplaced contigs (chr_Un..., UCSC ) in your reference. Finally you end up with a folder of FASTA files or a single FASTA file fully describing your reference chromosomes/contigs. This FASTA has to be converted to an index suitable for your mapping program. Most often it should be only a single command to to this conversion step. For instance in Bowtie you simply type:where REF_FASTA is the path to your reference FASTA (files).For every mapping with Bowtie against this reference you have to provide the path to this index, as it is in fact just another representation of your reference FASTA.Hope this helps