Question: How to get the extended unaligned bases at the end of the read in reference based genome assembly?
gravatar for Dineshkumar K
14 months ago by
Kasaragod, Kerala, India
Dineshkumar K40 wrote:

Hi all, I had done a illumina read mapping based on a particular gene sequence (reference sequence), which is highly repetitive in nature by 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 | vcf2fq > cns.fastq && seqtk seq -aQ64 -q20 -n N cns.fastq > contig.fasta

It is works perfectly fine and yielded exactly same length of mapped sequence as ref_gene. However, I need to get both end (reverse and forward end) extended overlapping reads in the assembled contig (Please see the image for better understanding) Is there any way to do it the same? enter image description here Thanks in advance.

ADD COMMENTlink modified 14 months ago • written 14 months ago by Dineshkumar K40
gravatar for WouterDeCoster
14 months ago by
WouterDeCoster44k wrote:

If I understood your question correctly you are looking at unaligned bases at the end of reads. That means you have to extract the soft clipped bases. Googling for that brings up this thread: extracting the soft clipped seq only from a sam file

ADD COMMENTlink written 14 months ago by WouterDeCoster44k

Thank you @WouterDecoster for your suggestion and giving me the proper technical word for the same.

ADD REPLYlink written 14 months ago by Dineshkumar K40

Dear @WouterDeCoster, the tool you have suggested only gives the mapped/aligned reads (exactly same length as reference). It is not giving the unaligned overlapped reads.

ADD REPLYlink written 14 months ago by Dineshkumar K40

I suspect you're looking at the wrong file.

ADD REPLYlink written 14 months ago by Devon Ryan97k
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