User: huiwenteh
huiwenteh • 0
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Posts by huiwenteh
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C: Bowtie2 aligning output
... means that I run my raw reads by using pairwise alignment and then straight variant calling?
...
written 4 months ago by
huiwenteh • 0
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C: Bowtie2 aligning output
... If I would be using pairwise alignment would I be able to preform variant calling? ...
written 4 months ago by
huiwenteh • 0
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C: Bowtie2 aligning output
... 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. ...
written 4 months ago by
huiwenteh • 0
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C: Bowtie2 aligning output
... 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 :) ...
written 4 months ago by
huiwenteh • 0
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C: Bowtie2 aligning output
... Hi, my sequence length is around 4MB. Any suggestion for multiple sequence alignment? ...
written 4 months ago by
huiwenteh • 0
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... 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.
$ bo ...
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... Hi, I am using mummer for alignment and snp calling. Now I have my list of snps but I am stuck at this current step which is to visualize the coverage of the sequence. This is to confirm that the snps are really snps not some background noise or other factor. Any suggestion of visualization tool I c ...
written 8 months ago by
huiwenteh • 0
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