Tool: DASHR 2.0: integrated database of human small non-coding RNA genes and mature products
0
gravatar for pkouxa
22 months ago by
pkouxa0
pkouxa0 wrote:

DASHR (Database of small human non-coding RNAs) v2.0 provides a complete catalog of annotation, expression, processing, conservation, tissue-specificity and other biological features for all human small non-coding (sncRNA) genes, full sncRNA transcripts and mature products derived from all major small RNA classes, including miRNAs, piRNAs, sc-, sn-, sno- RNAs, tRNAs, tRFs (https://lisanwanglab.org/DASHRv2 ).

DASHR 2.0 is an extremely useful resource and reference for the community studying non-coding RNAs and their diverse roles in often tissue-specific cellular processes related to human diseases.

Some of the DASHR v2.0 highlights include:

1) Integration of the largest collection of >180 tissues and cell types from ENCODE and curated GEO/SRA experiments (>22 billion reads) across multiple RNA-seq protocols for both GRCh38/hg38 and GRCh37/hg19 (http://dashr2.lisanwanglab.org/search.php );

2) The first database to profile both known sncRNA loci and novel, previously un-annotated sncRNA loci identified by de novo by genome-wide unsupervised segmentation (>1,600,000 small RNA loci; http://dashr2.lisanwanglab.org/search.php ) ;

3) Integration of >3,200,000 annotations for non-small RNA genes and other genomic features (e.g., long-noncoding RNAs, promoters) (http://dashr2.lisanwanglab.org/download.php );

4) Introduction of an enhanced user interface, interactive experiment-by-locus table views for easy sorting and filtering of small RNA loci data (http://dashr2.lisanwanglab.org/browse.php );

5) Access to genome wide expression tracks and called small RNA peaks freely downloadable (http://dashr2.lisanwanglab.org/download.php) and viewable in the UCSC Genome Browser (http://dashr2.lisanwanglab.org/browse.php ).

DASHR v2.0 database is freely available at https://lisanwanglab.org/DASHRv2.

DASHR v2.0 has been published in Bioinformatics.

Kuksa, Pavel P., Amlie-Wolf, A., Katanic, Z., Valladares, O., Wang, L., Leung, Y. DASHR v2.0: database of small human noncoding RNAs in human tissues and cell types. Bioinformatics, 2018. https://doi.org/10.1093/bioinformatics/bty709

ADD COMMENTlink modified 22 months ago by WouterDeCoster44k • written 22 months ago by pkouxa0

Hi,

I need to analysis GSM3139648. First of all, I had to trim that and after that, I aligned it to the reference genome by Bowtie. The result of alignment is good(SRR7155472_1.sam ) and now I would like to prepare for my count file. So, I used dashr.v2.annotation.hg38.gff as an annotation file for non-coding RNA based on the below code:

featureCounts  -M -f -O -s 0 -g ID -T 40 -t piRNA -a  dashr.v2.sncRNA.annotation.hg38.gff  -o  SRR7155472_feature_count_custom_gene_nonunique.count      SRR7155472_1.sam

but I got below result:

Reading data from <STDIN> for featureCounts ...

||    Meta-features : 30882711                                               
||    Chromosomes/contigs : 24                                              
||                                                                                                   
|| Process SAM file SRR7155472_1.sam...                            
||    Single-end reads are included.                                        
||    Assign alignments to features...                                       
||    Total alignments : 15892776                                            
||    Successfully assigned alignments : 0 (0.0%)                   
||    Running time : 5.50 minutes

As you see, the result is not suitable. I appreciate if you share your comment with me and guide for my problem.

ADD REPLYlink modified 13 months ago • written 13 months ago by modarzi130
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1931 users visited in the last hour