Bowtie2 aligning output

Question

[huiwenteh]

Hi, I am currently using bowtie2 to align my sequence. I am using a assembled sequence to align with my reference sequence.Unfortunately, the output after aligning is stated as killed and error. I am currently stuck in this situation. Below is my command line which is inserted and the output.

$ bowtie2 -f -x Mycobacterium -U R1_final.contigs.fa -S R1.sam Killed (ERR): bowtie2-align exited with value 137

I am not sure what is the problem and how to solve it. I hope I can get some help here :)

p/s: I am still abit new to bioinformatics and so sorry for the inconvenience caused :)

Cheers, HuiWen

[Arup Ghosh]

I think you are looking for multiple sequence alignment. Bowtie2 supports reads up to 1000 bp. What's the length of of your assembled sequence?

[huiwenteh]

Hi, my sequence length is around 4MB. Any suggestion for multiple sequence alignment?

[Asaf]

You don't need Multiple Sequence Alignment, just pairwise alignment.

[huiwenteh]

If I would be using pairwise alignment would I be able to preform variant calling?

[Asaf]

You better use the raw reads, not the assembly in that case

[huiwenteh]

means that I run my raw reads by using pairwise alignment and then straight variant calling?

[Asaf]

I strongly recommend properly training on how to do that, it's a complex topic. You might want to collaborate on this aspect.

Answer 1

[Asaf]

As Arup mentioned, Bowtie2 is meant for short reads mapping, not assembly contigs. You can try other software like minimap2 or mummer.

[huiwenteh]

Hi, I tried mummer before to align and SNP calling but I got stuck when it comes to visualize the SNPs. Due to mummer produce delta file, I wasnt able to convert delta file into sam/bam file to visualize it in IGV/bamview. Thank you for the suggestion on minimap2. I give this software a try :)

[Arup Ghosh]

What's your primary goal, variant calling or (pairwise/multiple) sequence alignment?

[huiwenteh]

my primary goal is variant calling. But if I continue my work with pairwise alignment is it possible to do variant calling after the pairwise alignment? Because to my best knowledge for variant calling we need to perform multiple sequence alignment. Correct me if I am wrong.