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I did illumina read mapping based on a particular gene sequence (reference sequence) using the following command,

bowtie2-build -f ref_gene.fasta ref_index && bowtie2 -p 4 -N 1 -t -x ref_index -1 genome_R1.fastq -2 genome_R2.fastq -S tal.sam && samtools view -bS tal.sam | samtools sort - -o tal.bam && samtools mpileup -uf ref_gene.fasta tal.bam | bcftools call -c | vcfutils.pl vcf2fq > cns.fastq && seqtk seq -aQ64 -q20 -n N cns.fastq > contig.fasta

It maps the reads according to the reference sequence and yields, exactly same length of aligned/assembled sequences. But, I need obtain the unaligned overlapping read bases at the both end (reverse and forward end) Please see the image for better understanding.

image of the reference gene and the extended read

Is there any way to get the same?

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    $\begingroup$ You're not going to get vastly different replies here than Biostars or github. $\endgroup$ – Devon Ryan Sep 27 '19 at 13:17
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    $\begingroup$ @DevonRyan sniper! $\endgroup$ – d_kennetz Sep 27 '19 at 21:42

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