Post mapping extract query sequence mapped to each gene feature

Question

[L_bioinfo]

I did a mapping on my query reads to the genome using bwa. I wish to extract the query sequence that matched with the gene feature. I found column 10 in samtools to provide information on the query sequence that matched to genome (which in many cases covers outside of gene feature).

Since, I am interested in extracting the query base sequence mapped only to the gene feature. Is there a possible way to perform I have been looking in seqkit locate and grep but they aren't feasible.

genome    mappedcoordinate_start    mappedcoordinate_end     query ID    gene_ID    gene_start      gene_end
Xgenome    26                       3000                     read_1      gene_1        30      740

I want to extract the query sequence corresponding to chr:30:740 instead chr:26-3000. I have 2 million hence I need a tool can't do this manually.

I need the query sequence as we decided to probe on it.

Appreciate all help.

[Pierre Lindenbaum]

. I wish to extract the query sequence that matched with the gene feature

What do you mean ?

[L_bioinfo]

The mapping was performed between the query reads and the reference genome. I have long read sequences and they cover more than one gene at time within the genome. I want to extract query sequences that mapped to each particular gene.

[Pierre Lindenbaum]

do you want https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker ? using -L your.gene.bed ?

[GenoMax]

If you are interested in extracting all query sequences that fall within a region (gene) then you can try this: Isolating reads from specific region from bam file

samtools ampliconclip may also be applicable if you want to truncate the reads (http://www.htslib.org/doc/samtools-ampliconclip.html )