Tweet
Hi,
How can I set for the best 10 hits when blasting with command line blast?
kaps
How can I set for the best 10 hits when blasting with command line blast?
kaps
-
-
Did you try
?Code:-max_target_seqs 10
"Best" doesn't mean the same thing to everyone - but max_target_seqs should select the hits with the highest e-value and bit score. -
yes,
but its like -max_target_seqs 10 does not give 10 maximum hits since i am getting many hits, more than 10!!Comment
-
Could you post the results? Often you get several (partial) alignments against one database sequence, which then counts as one "target sequence".Comment
-
Attached is a txt file with the results.
I wait for your comments!Comment
-
As far as I can see, there are only one query with more than ten result lines (query 4_S4_L001_R1_001_(paired)_trimmed_(paired)_contig_23); in that case, one database target sequence has two alignments. This is the expected behaviour.Comment
-
You are getting the 10 best target sequences for each query. For some of the queries, there is more than one hit (hsp) to the target. Those are returned too, so sometimes there are more than 10 lines per query. This is good behavior, e.g. if your query is cDNA and the target is a gene with an intron, the query is split into two matches.Comment
-
Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...07-09-2026, 11:10 AM -
Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.
There is no single reason why many patients don’t respond to treatment as expected. Cancer is...07-08-2026, 05:17 AM -
Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
Comment