Question: Interpreting Flags in SAM file
1
gravatar for jayg
3.3 years ago by
jayg10
jayg10 wrote:

Hi,

I have Illumina pair ended reads mapped to contigs. All the pair ended reads have innie (------> <----------) orientation. I want to find orientation of contigs inferred from reads. Please see following cases

  1. When the read is first in pair and is mapped to forward strand:

----------------------------------> contig

------------> read

  1. When the read is first in pair and mapped to reverse strand:

<---------------------------- contig (rev complemented)

-----------> read

  1. When the read is second in pair and mapped to forward strand:

<---------------------------- contig (rev complemented)

<------------

  1. When the read is second in pair and mapped to reverse strand:

------------------------------> contig

<------------ read

Is the correct way to interpret?

Thank you very much.

illumina sam assembly • 1.2k views
ADD COMMENTlink modified 3.3 years ago by Pierre Lindenbaum121k • written 3.3 years ago by jayg10
1

It is not entirely clear what you are asking:

samtools flags

will tell you all the flags that you can use. Then you can add that to the -F and/or -f as needed (you can combine into a single number but sometimes is more explicit to list each separately). For example reads that are: mapped, first in pair, forward strand

-F 4 -f 64 -F 16
ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Istvan Albert ♦♦ 80k
1
gravatar for Pierre Lindenbaum
3.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k wrote:

you're wrong with first and second in pair: first and second means that if the read comes from a paired-end experiment (output was something like R1.fastq.gz and R2.fastq.gz), then "1st in pair" was a read from R1.fastq.gz and "2nd in pair" came from "R2.fastq.gz". And that's it, there is no indication about the position.

ADD COMMENTlink written 3.3 years ago by Pierre Lindenbaum121k
0
gravatar for John
3.3 years ago by
John12k
Germany
John12k wrote:

Basically, it all comes down to if the sequencing was stranded - i.e. during PCR the original strand of DNA being amplified is some how recorded.

Maybe this post will help you: How many ways a read pair can be mapped?

ADD COMMENTlink written 3.3 years ago by John12k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1666 users visited in the last hour