iGenome indexes for Chimpanzee and Bonobo (panTro3)

Dear Biostars,

I am trying to map Chimpanzee and Bonobo RNA-Seq reads against their genomes by using TopHat. Do you know where can I find the indexes of these genomes ? thanx in advance.

bowtie tophat

• 3,358 views • link

updated 4.9 years ago by Ram

• written 12.2 years ago by biorepine

Have you been able to resolve mapping to the bonobo genome? I'm trying to do the same thing and haven't found a good reference genome to start with. I have seen some people map to PanTro4 instead. Any help would be much appreciated! Thanks!

• 0 views • link

written 12.0 years ago by sara.linker •

I haven't started building. Probably will start building them end of this month. Would you like to join along with me @sara?

• 1 views • link

written 11.9 years ago by biorepine

1 answer

The chimp index is available from iGenomes. You might have to build the bonobo one yourself (it's not difficult).

• 0 views • link

written 12.2 years ago by Devon Ryan

thanx. So how can I build bonobo index ? :P

• 0 views • link

written 12.2 years ago by biorepine

Tophat uses indices made by bowtie2, so just read through the help for bowtie2-build. You'll need a copy of the reference genome and a bit of time (it's just one command, but it takes a while to run).

• 0 views • link

updated 6.8 years ago by Ram

• written 12.2 years ago by Devon Ryan

More posts like this

alignment to a special part
written 9.1 years ago by alirezamomeni707 •

I have a RNA-seq data and want to get the proportion of reads that map to a window of `100pb` between `5'UTR` and `CDS` (`50 …
Mappping read to its exact postion in genome
written 10.2 years ago by EVR

HI, I would like to map the RNA seq reads to exact position from where it originated in genome USING TOPHAT, how could one achieve …
How to overlap transcription factor binding sites with unstranded transcript promoters
written 11.8 years ago by biorepine

Dear Biostars, I have a set of noncoding transcript genomic co-ordinates in BED format but with out strand information. I need to calculate the enrichment …
How to calculate phastcons scores for overlapping transcripts with different strands
written 12.3 years ago by biorepine

Dear Biostars, I am trying to calculate conservation scores for overlapping sense and anti-sense pairs of transcripts. Previously I used phastcons scores from ENCODE(mm9) to …
Fr-Secondstrand Versus Fr-Unstranded Library Type In Tophat2
written 12.5 years ago by biorepine

Dear biostars, Does any one have experience using fr-secondstrand versus fr-unstranded library types in tophat. I am running tophat against fr-secondstrand type rna-seq reads but …
How To Split Chr11 Bam File In To 2 Halves ?
written 12.6 years ago by biorepine

Dear Biostars I am aware of <a href='http://samtools.sourceforge.net/'>samtools</a> splitting of <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> file based on chromosome. But is there any way I can divide a …
How To Calculate Base-Level Read Coverage Of Each Transcript ?
written 12.7 years ago by biorepine

Dear Biostars, I am trying to remove the transcripts that have less than 0.1 average base-level read coverage. But I am quiet confused with calculation …
Where Can I Download Pirna (Piwi Rnas) Of Mouse (Mm9)
written 12.8 years ago by biorepine

Dear Biostars Does some one know where can download mm9 piRNAs in BED or GTF format ? Thanx in advance
Manual Transcriptome Reconstruction Using Rna-Seq Reads (Hg19)
written 12.9 years ago by biorepine

Dear Biostars, I have been reconstructing novel coding or non-codng transcripts using either <a href='http://cufflinks.cbcb.umd.edu'>Cufflinks</a> or <a href='http://www.broadinstitute.org/software/scripture/'>Scripture</a> from 2 years. They are very efficient …
How One Can Separate Noncoding From Coding Ucsc And Ensembl Transcripts
written 13.2 years ago by biorepine

Dear biostars, Do you know how one can separate noncoding from coding UCSC and ENSEMBL transcripts ? In general I use NR_* to identify …