Hi all,
I have fastq files having Illumina paired end sequence reads. I want to align a part of read say read length is 75 bases and I want alignment in which at least 50 bases are aligned without any gap in between.
Why do I want this type of alignment is because there is a fusion of target sequence with reference sequence, so I want to ignore all completely aligned reads with reference and want to find out reads in which a part of target sequence is covered. (for example, as per above given calculation, out of 75 bases, I want to detect all reads having 25 bases from target sequence and 50 from reference sequence.
I tried with trimming the sequence and than aligning them separately but that is not working.
Is there any alignment tool which allows me to do alignment of 75 bases reads with parameters like align first 50 bases or last 50 bases with reference so that I can retrieve them and than align remaining bases with target sequence.?.?.?
Thanks in advance.
I have fastq files having Illumina paired end sequence reads. I want to align a part of read say read length is 75 bases and I want alignment in which at least 50 bases are aligned without any gap in between.
Why do I want this type of alignment is because there is a fusion of target sequence with reference sequence, so I want to ignore all completely aligned reads with reference and want to find out reads in which a part of target sequence is covered. (for example, as per above given calculation, out of 75 bases, I want to detect all reads having 25 bases from target sequence and 50 from reference sequence.
I tried with trimming the sequence and than aligning them separately but that is not working.
Is there any alignment tool which allows me to do alignment of 75 bases reads with parameters like align first 50 bases or last 50 bases with reference so that I can retrieve them and than align remaining bases with target sequence.?.?.?
Thanks in advance.
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