Tool:DASHR 2.0: integrated database of human small non-coding RNA genes and mature products

Question

[pkouxa]

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

[modarzi]

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.