User: elesbb91

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elesbb910
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Posts by elesbb91

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Comment: A: Blastn command line tab format gives duplicates
... So I figured it out. Thank you guys. The second hits were partial alignments of the same strand as JC posted. So I understand now the differences. Thank you everyone! ...
written 7 hours ago by elesbb910
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Comment: C: Blastn command line tab format gives duplicates
... Yes, I do not have two alignments in my standard format. I only see the two in the tabular format. This is the whole problem lol. I have no idea why. I also do not see both alignments in the online blast either, even if I download the results. ...
written 1 day ago by elesbb910
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Comment: C: Blastn command line tab format gives duplicates
... In standard output, I do not see both alignments either in the summary nor in the pair-wise alignments. This goes for the HTML version too. Even the link you provided I am only seeing one hit for XM_017006782.1 as well as in the alignments view. I seriously am so lost xD NVM I see them. So they are ...
written 1 day ago by elesbb910
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Comment: C: Blastn command line tab format gives duplicates
... Take a look at my comment, I just don't understand how changing the output format will change the hits too ...
written 1 day ago by elesbb910
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Comment: C: Blastn command line tab format gives duplicates
... For example, XM_017006782.1 is listed twice in tab format but NOT in standard format. ...
written 1 day ago by elesbb910
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Comment: C: Blastn command line tab format gives duplicates
... So, this is all great news and stuff.. But, why when using standard output (not adding the output parameter) those other hits are not included? If I use `-outfmt 7` I get more hits? Like, a heckin load more. It seems odd because the ONLY thing that is changing is the outfmt.. My only guess is that ...
written 1 day ago by elesbb910
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Blastn command line tab format gives duplicates
... When using the tab output format, it causes multiple outputs of the same hit to show, but with different %identities and other attributes. When using the standard output, the results are what I find on the web based version of the blastn tool. How can I create a tabular form of results without get ...
command-line blastn written 2 days ago by elesbb910
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Comment: C: NCBI Blastn+ command line - How do I limit to a specific TSA project or organism
... Well that is an easy solution!! Thanks so much! ...
written 16 days ago by elesbb910
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NCBI Blastn+ command line - How do I limit to a specific TSA project or organism?
... I am usign blastn+ to do some batch processes and to go through the tsa_nt database. However, I need to limit to specific taxids. If I use `taxids` parameter I am told that taxids do not work on blast databases v4. But I need to limit the search to either a TSA project, or the specific organism. How ...
ncbi assembly written 17 days ago by elesbb910 • updated 17 days ago by genomax78k
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Answer: A: BLAST Database error: Error pre-fetching sequence data
... Okay, @genomax, So I didn't include -parse_seqids. And when I type the command: `blastdbcmd -db RNA_HUMAN -entry NR_118908.1` I get: `Error: [blastdbcmd] DB contains no accession info.` Out of curiosity I downloaded v2.9.0+ and and using that makeblastcmd everything works. Including the `-parse_s ...
written 4 weeks ago by elesbb910

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Scholar 29 days ago, created an answer that has been accepted. For A: BLAST Database error: Error pre-fetching sequence data

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