quantify how many reads detect ORF9 and ORF10

Question

[mkhatun]

Hi there,

Is there any way to quantify how many reads detect ORF9? I have a word doc with the different parts annotated and sequences of ORF9. I don't have any bam file or other reference file.

Any kind of help regarding how I can get reads by using these information would be awesome.

Thank you so much in advance!

[Pierre Lindenbaum]

you "don't have any bam" but you want "to count he number of reads" ?(!)

Answer 1

[seidel]

Yes. Remove ORF9 from word and place it in a text file in fasta format (google it). Convert this file to an alignment index for your favorite aligner. Use your favorite aligner and the index you just made and align your reads to generate a BAM file. Use samtools to count the reads in your BAM file that align to your ORF9 reference.

[mkhatun]

Thank you so much seidel for your response. I want to use igv aligner (need reference and Bam file) and get the image (attached) regarding the alignment. I already made the reference file based on my ORF9 sequences. Could you please describe briefly how i can get the BAM file using these annotated parts?

Thanks again for your help! Khatun