HISAT2 Genome indexing

Question

[HaroonPakistan]

Hi, I am new to bioinformatics. I wanted to do the mapping. I have done the indexing of gnome. It created 8 output files. I don' know is it ok or not? please check it! t

[Medhat]

I changed this to a question, please try to add the files as a list not as a picture, for better visualization.

[HaroonPakistan]

index_name.1.ht2 index_name.2.ht2 index_name.3.ht2 index_name.4.ht2 index_name.5.ht2 index_name.6.ht2 index_name.7.ht2 index_name.8.ht2

[Kevin Blighe]

Hello, Muhammad. Can you now perform the alignment step using this [purportedly] indexed reference genome? Doing this will permit that you can then infer whether or not the genome was indexed correctly. Also, can you let us know whether or not the command to index [the genome] completed without any warning or error messages? Thank you.

[HaroonPakistan]

indexing was completed successfully. Can you write the next command. I have paired-end data. So, I have forward and reverse paired and unpaired fq files. Now, I am confused about how to arrange the data. And what should I put in the name of the index file because there are many indexing files?

[HaroonPakistan]

output_b73_forward_paired.fq output_b73_reverse_paired.fq output_f1_forward_paired.fq output_f1_reverse_paired.fq output_mo17_forward_paired.fq output_mo17_reverse_paired.fq output_b73_forward_unpaired.fq output_b73_reverse_unpaired.fq output_f1_forward_unpaired.fq output_f1_reverse_unpaired.fq output_mo17_forward_unpaired.fq output_mo17_reverse_unpaired.fq

I have these RNA-seq files, both paired and unpaired. Do I need to map one by one or all together? Furthermore what about the unpaired data?

[HaroonPakistan]

Furthermore, these are eight indexed files. Do I need to put in the command one by one?

[gglim]

Type hisat2 --help and check the usage

HISAT2 version 2.0.4 by Daehwan Kim ([e-mail], www.ccb.jhu.edu/people/infphilo)
Usage: 
  hisat2 [options]* -x <ht2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <sam>]

  <ht2-idx>  Index filename prefix (minus trailing .X.ht2)......

[HaroonPakistan]

and what is this ? -U <r>

[gglim]

that's for single-ended data. Try explore the help message on your own server

[HaroonPakistan]

Hi, can you write a command for Alignment?