Hi all,
I am beginner to bio-informatic field. I have posted several types same question to get the help to understand the way to analyze the bowtie results. I have a paired viral read. To which I aligned it to the viral reference genome. For paired read I have one SAM output. My main objective is what portion of the reads aligned to the reference genome. For that, I analyzed the bowtie result from SAM report. Is it okey to use the column first and third of SAM report to interpret that the reads displayed in the first column aligned to that particular reference genome in the third column?for my understanding for the Bowtie results is that the first represents the read that aligned and third column represents the name of the reference sequence where alignment occur.
I really need help to understand here. I do not have any template for bowtie results analysis.
Regards, Bandana
Have a look at the sam file specifications and see if that answers your question.
Thank you. But still, I am unable to interpret the SAM report fully.
Bowtie is old and there are better alternatives for most uses. You should never use Bowtie unless you are aligning extremely short reads, ~36bp or less. Do you, perhaps, mean Bowtie2?
Yes, I am using Bowtie 2 and my reads are about 45bp-76bp. I have the SAM output . What I am trying to figure out is, how many reads aligned to the reference.I am not able to understand the SAM manual which says about the tabular format output.Is it okay to make interpretations using the tabular SAM output?
Bowtie2 probably prints the number of aligned reads in its output somewhere. Alternately, you can use BBMap like this:
The "Output:" line will tell you the number of mapped reads.
If paired reads are used, then bowtie will print for both reads one alignment per line or it will print for each individual reads? I am confused with paired reads data analysis.Please can you help me with this?
Each alignment gets its own line. Each read can have zero or more alignments. For a pair of reads, if they each align once, you get 2 lines.
Thank you soo much.
Do I need to check for the flag in second column while looking for the alignment?
The flag tells you thinks like whether the read was aligned to the plus or minus strand, so yes, it is important. You can copy and paste it here for an explanation:
https://broadinstitute.github.io/picard/explain-flags.html