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Thread: Kmer tool
Post: RE: Kmer tool
| Hi Rosario,
The kmer tool requires that your Ribo-seq data to be mapped to the a genome and not the transcriptome.
Normally I would say that your gff3 file is correct. I presume from that you obtain... |
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audrey |
RiboGalaxy |
4 |
304 |
05-Oct-2017, 08:59 AM |
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Thread: Ribo-SeqR input preparation
Post: RE: Ribo-SeqR input preparation
| Hi Rosario,
It is a good question.
I think it would be best to initially run the riboSeqR tool on each SAM file separately so that you can get a sense if the triplet periodicity/metagene analysis is... |
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audrey |
RiboGalaxy |
1 |
58 |
04-Oct-2017, 04:21 PM |
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Thread: big peak at maximum sequencing length
Post: RE: big peak at maximum sequencing length
| Hi Beth,
Just so that we understand better, the reads of length 51nt have been trimmed of adapter sequence?
What are the lengths of your raw reads before removing adapter? |
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audrey |
Ribosome profiling protocol |
4 |
1,732 |
31-May-2017, 10:30 AM |
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Thread: big peak at maximum sequencing length
Post: RE: big peak at maximum sequencing length
| Hi there,
I haven't observed a peak at 51nt before.
If the full length of your sequence reads is 51nt, then presumably these reads do not have any adapter sequence?
Do they map to coding regions i... |
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audrey |
Ribosome profiling protocol |
4 |
1,732 |
31-May-2017, 07:59 AM |
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Thread: How to get a bam file
Post: RE: How to get a bam file
| Hi there,
The conversion of the sam file to bam format requires the reference sequences FASTA (genome or transcriptome) to which the reads were mapped.
We are perplexed as to why the rRNA sequences ... |
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audrey |
RiboGalaxy |
5 |
1,750 |
18-Apr-2017, 09:18 AM |
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Thread: genome request
Post: RE: genome request
| Hi Beth,
The genomes that we have listed correspond to genomes that we have in GWIPS-viz so that user data mapped to these genomes can be explored in the context of published data.
However, you can ... |
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audrey |
RiboGalaxy |
1 |
369 |
12-Apr-2017, 09:13 AM |
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Thread: upload via ftp
Post: RE: upload via ftp
| Hi there,
You could try using an FTP client tool such as FileZilla to upload the data. Some slides on the usage of FileZilla to upload to RiboGalaxy are provided on the 'RiboGalaxy demo slides' on th... |
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audrey |
RiboGalaxy |
1 |
712 |
02-Mar-2017, 10:16 AM |
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Thread: frames
Post: RE: frames
| Hi Mike,
For the metagene plot, the value(s) entered for the 'Frames of the ribosome footprint reads to be used in filtering' are usually taken from the triplet periodicity results where the likely f... |
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audrey |
RiboGalaxy |
1 |
707 |
24-Jan-2017, 04:26 PM |
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Thread: Ribo-seq coverage data
Post: RE: Ribo-seq coverage data
| Hi
There are two ways you can access the count data which are displayed in the ribosome profile graphs.
The Downloads tab http://gwips.ucc.ie/downloads/index.html provides the count data in bigWig ... |
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audrey |
Bioinformatics |
1 |
1,699 |
08-Dec-2016, 01:52 PM |
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Thread: config file error in triplet periodicity
Post: RE: config file error in triplet periodicity
| Hi,
Just to confirm that the Triplet Periodicity tool only generates one plot.
To generate separate triplet periodicity plots for your wildtype duplicates and your mutant duplicates, the best would ... |
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audrey |
RiboGalaxy |
2 |
2,679 |
04-Jul-2016, 12:47 PM |
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Thread: stuck: triplet periodicity
Post: RE: stuck: triplet periodicity
| Hi there,
The error is likely originating from the spaces in your fasta headers (>I space dna ... etc) because in your SAM file, the alignments are to the chromosomes (i.e. the entries in your fas... |
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audrey |
RiboGalaxy |
8 |
1,984 |
08-Feb-2016, 05:29 PM |
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Thread: Question about Stadler&Fire's mRNA data
Post: RE: Question about Stadler&Fire's mRNA data
| Hi szhang,
Apologies, we only noticed your second question just now.
We confirm that we have not made any changes to the mRNA data of HeLa Stumpf 2013 in GWIPS-viz.
Kind Regards,
Audrey |
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audrey |
Tracks in GWIPS-viz |
3 |
2,353 |
01-Feb-2016, 10:02 AM |
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Thread: Question about Stadler&Fire's mRNA data
Post: RE: Question about Stadler&Fire's mRNA data
| Hi szhang,
The Stadler&Fire HeLa mRNA-seq data from (http://www.ncbi.nlm.nih.gov/sra/SRX118141[accn] and http://www.ncbi.nlm.nih.gov/sra/SRX118142[accn]) were combined into a single track in GWIP... |
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audrey |
Tracks in GWIPS-viz |
3 |
2,353 |
27-Jan-2016, 01:59 PM |
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Thread: Mapping parameters
Post: RE: Mapping parameters
| Hi Renana,
The mRNA-seq reads can vary in length from study to study. For GWIPS-viz mRNA-seq coverage profiles, the only restriction for the mRNA-seq reads alignment is that they are of minimum lengt... |
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audrey |
Tracks in GWIPS-viz |
2 |
1,721 |
04-Jan-2016, 11:25 AM |
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Thread: How to use GWIPS for viewing personal bam file
Post: RE: How to use GWIPS for viewing personal bam file
| An update to this question, BAM files can now be directly uploaded as custom tracks in GWIPS-viz.
Use the format
track type=bam name="bam Example One" description="A bam file" bigDataUrl=http://geno... |
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audrey |
Tracks in GWIPS-viz |
3 |
3,466 |
04-Jan-2016, 10:33 AM |
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Thread: cram file format
Post: RE: cram file format
| Hi,
CRAM file format is not currently supported in RiboGalaxy. However we will look into this and thank you for bringing it to our attention.
Thanks. |
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audrey |
RiboGalaxy |
2 |
1,596 |
19-Nov-2015, 06:32 PM |
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Thread: Triplet Periodicity
Post: RE: Triplet Periodicity
| Hi Yingpu,
You can generate metagene plots with the Metagene Analysis tool in the riboSeqR suite of tools (Step 3). After aligning to your transcriptome, you will need to run steps 1 step 2 in riboS... |
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audrey |
RiboGalaxy |
12 |
5,882 |
02-Nov-2015, 09:25 AM |
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Thread: Brar 2012 data - table-specific information
Post: RE: Brar 2012 data - table-specific information
| Hi Renana,
You are correct that when you click on the "describe table schema" link in the Tables Browser, all of the GEO accessions are provided. We do not provide the GEO accessions for the individu... |
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audrey |
Tracks in GWIPS-viz |
1 |
1,678 |
27-Jul-2015, 09:39 AM |
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Thread: Fontconfig error
Post: RE: Fontconfig error
| (13-Jul-2015 05:48 PM)ghg296 Wrote: Hi,
I am attempting to run the triplet periodicity test for my data. I have managed to upload my .sam file and convert it to the R input format. Unfortunate... |
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audrey |
RiboGalaxy |
4 |
2,913 |
14-Jul-2015, 08:17 AM |
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Thread: colorectal cancer ribo-seq data
Post: RE: colorectal cancer ribo-seq data
| Hi Joana,
There is ribo-seq data on HCT116 cells available on NCBI GEO datasets GSE58207 ( http://www.ncbi.nlm.nih.gov/geo/query/ac...c=GSE58207 ).
This data is not yet in GWIPS-viz. However, the be... |
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audrey |
RiboGalaxy |
2 |
4,455 |
25-May-2015, 08:52 AM |
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