How start with own mapped bam, genome and annotation file

[abarthol]

Hi,

is it possible to start with an own results from mapping giving also information about the annotation (gene feature in bed or gff) and the genome in fasta format?

If not are you planning it, or is it too incompatible because you cannot ensure correctness of uploaded data?

Best,
Alex

[jamesp]

Hi,
if you have a mapped bam file, you could upload it and then try to use either of the tools "Generate ribosome profile from bowtie output (RNase 1 data) from Bowtie output file converted to BAM" or "Generate ribosome profile from bowtie output (MNase data) from Bowtie output file converted to BAM" in the group of tools "GWIPS-viz mapping". Either tool will produce two files, a ribosome profile and a ribosome coverage. Both of these files can then be visualized in GWIPS-viz.

Regards
jamesp

[MaximilianAnders]

Hi Jamesp,

we have also tried using our own mapped data using your suggestion.

When it comes to choosing a fitting transcriptome in step II of the riboseq analysis we are puzzled, which one to choose, as none is provided?

Since we are mapping to the genome, we never needed a transcriptome using our conventional methods.

Here, it seems a transcriptome needs to be selected though.


Do we have to provided our own? And if so, which format should it be in and how do we produce it?


Thanks,

Max

[vimalkumarvelayudhan]

Hi Max,
With regards to your question on transcriptome and ribo-seq analysis, you will need to provide a FASTA format file of the transcriptome.
If you do not have this, please check the RiboGalaxy help page under "Alignments to a transcriptome" for a method to obtain the transcriptome from UCSC.

Once you have the transcriptome, please follow these steps to pre-process, align RiboSeq/RNASeq data (fastq) to the transcriptome and perform RiboSeq Analysis.

1. Pre-processing tools -> Cutadapt
2. Pre-processing tools -> Remove rRNA using Bowtie
3. Transcriptome Mapping -> Align to transcriptome using Bowtie
   
   Select the reference transcriptome obtained from UCSC.
   
   The output will be a SAM file.
4. RiboSeq Analysis -> Prepare riboSeqR input
   
   Select the SAM format file from step 3.
5. RiboSeq Analysis -> Triplet Periodicity
   
   Select "Prepare riboSeqR input (R data file)" produced from step 4.
   
   Under findCDS parameters, select the transcriptome obtained from UCSC.
   

Regards,
Vimal

(20-Jul-2015 11:51 AM)MaximilianAnders Wrote:  Hi Jamesp,

we have also tried using our own mapped data using your suggestion.

When it comes to choosing a fitting transcriptome in step II of the riboseq analysis we are puzzled, which one to choose, as none is provided?

Since we are mapping to the genome, we never needed a transcriptome using our conventional methods.

Here, it seems a transcriptome needs to be selected though.


Do we have to provided our own? And if so, which format should it be in and how do we produce it?


Thanks,

Max