how would I get all the LncRNA of human which are reported and their position on chromosome based on first and last nucleotide ?
I would check out Ensembl's BioMart, it might be what you are looking for.
1. Go to www.ensembl.org/biomart
2. Select Ensembl Genes
3. Select human genes, if you're working with humans. Please note, it will state the assembly and patch (e.g. GRCh38.p10). If you are looking for the positions for another release such as GRCh37/hg19, the coordinates will be off.
4. Click Filters (far left side)
5. Click gene
6. Scroll to gene type
7. Click lincRNA
8. Click Attributes (far left)
9. Click all the goodies you would like reported. For example, you may want "Gene start (bp)", "Gene end (bp)", chormosome, gene name, etc.
10. Once your ready for the report, in upper left corner, click results
11. Near "Export all results to", click "compressed file (.gz)". If the results are too big and there's an interruption, the decompression of the .gz file will likely inform you that you will need to try again. If you are still having issues, you can use the filter (left side) to break it into small chunks, such as downloading it by chromosome.
12. Click Go and enjoy!
Hope it helps.
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