Indexing reference genome hg.19 ?

[vishnuamaram]

Hello everyone,

I am very new to this seqanswers community.

Regarding my question

Information:-

1) I have whole genome sequence data of human lymphocyte done on illumina hiseq2000 paired end with 2X100bp readlength in FASTQ format
2) I have run FASTQC of my data and based on the quality, i had trimmed bases with low quality using FASTX toolkit.

3) I have downloaded refhumangenome hg19 from UCSC.

Q). My question is how to index ref genome, what does indexing do exactly.
Do we need to consider even the Chr un...... files also for indexing or not.
As i really dont know how to proceed from here. i am struck with performing further analysis. Guys, kindly let me know the answer as soon as possible.

[Heisman]

What type of experiment have you done? indexing the genome is a requirement to use many aligners in the field, so if you want to align your data to a reference genome you can pick an aligner of choice (ie, Bowtie2) and then download/install it and it will have a program that can index the genome for you. Do you have any idea at all how to analyze the dataset you've been given? Do you have anybody nearby you can talk to in person about analyzing your dataset? If not I would try to find some reviews relevant for the type of experiment you've done that can give you an overview of how to analyze the data.

[vishnuamaram]

Hi Heisman,

Thats very nice of you responding to my message. I request an apology for my delayed response.

Yes, there are people who can guide me. They are experts with regard to the bacterial genome analysis.

At present, I am done with alignment of my whole genome sequence of human sample by BWA. I got the SAM files of the data.
--> I would like to finally look for SNP's and if possible structural variations like indels, CNV's etc.

--> Other than SAMTOOLS, what other software tools will be required for the further downstream analysis. Kindly let me know.

Thank you,
Vishnu.