3.3 years ago by
UK, Hinxton, EMBL-EBI
I'd recommend very much the opposite: do use filters. The more the better actually. BioMart is not the tool to retrieve all the human genes (or transcripts) or their sequences or anything genomewide. Hence you've got the 'warning' max 500 advised to input your data (list of gene IDs for example). Also the only format to download the sequences is FASTA. There will not be a TSV.
The likely reason you only got 1000 sequences is the the web timed out due to the huge numbers of results it had to process. If you want to use the web interface I'd recommend you to do the query in chunks (per chromosome for example, selecting a filter under REGION). You can also try to get the results in a compressed format sent to you by email (when it's ready). That one should have all the sequences you are after and not 'just' the first 1000.