Finding the right database for blast CLI
We are looking into the possibility of off-target mapping for some sequences that were added to our alignment reference. We are only concerned about off-target mapping to genes (including introns). We are also only concerned about off-target mapping in mouse.
To look at this I want to do a blast search on ~1000 sequences that mapped to our added sequence, only to the mouse genome and only to genes (including introns). I have a fasta file for mm10 and a gtf file describing the genes, but I am unsure how to put this into blast + (blast CLI) so that I know that I am searching genes.
Thanks!
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Normalization of RNA captureSeq data (<20 genes captured)
written by jips •
-
customized gene not show in the output from cellranger count even if I have added to the reference …
written by leranwangcs •
-
Troubleshooting contamination in ChIP-Seq
written by Zemmiphobe •
-
Mapping different mouse strains to mm10
written by Assa Yeroslaviz
-
How to specify Cut-off/parameters of sequence identity > 70% and query length > 40% in BLAST comman…
written by Kumar
-
Forum: Tool for miRNA target prediction and translation from mouse to human?
written by passi.g •
-
CLCBio Genomics workbench - protein coding genes only
written by Annika Forsingdal
-
Using R to "NCBI Blast" query DNA sequence automatically, many sequences to do
written by Megatron •
-
Viable pathway tool for T-Cell activation pathway identification
written by onspotproductions
-
Mapping target-enriched reads to a transcriptome reference
written by matt.christmas85 •
You can make your blast database using
makeblastdband align your sequences against that database. Use-outfmt 6for the output. Convert tabular blast+ output to BED format (Convert blast tabular output to bed format ). Then you can intersect BED output with a BED file for gene models.A command line manual for blast+ is available here.