Bowtie2 not putting /2 /1 at the end of paired reads in SAM file

Question

[SaltedPork]

Hi,

My command is:

bowtie2 -x bowtie.db -1 $sample.host.removed.R1.fastq -2 $sample.host.removed.R2.fastq -S $sample.consensus.align.sam

It outputs a SAM file with read IDs like:

M03972:384:000000000-KDHHW:1:1101:22168:9677

However, in the input reads files there is a /1 or /2 on the end of the read. Is there a way of printing this to the SAM file?

Answer 1

[Istvan Albert]

The SAM flag will contain the information on whether the read is from file 1 or file 2.

The SAM spec explicitly notes that read names must be identical for them to be considered paired.

Reads/segments having identical QNAME are regarded to come from the same template

The /1 and /2 naming scheme comes from an older generation of instruments and is an artifact of the past.

[SaltedPork]

ah okay, thanks. How will I know which is forward, and which is reverse?

[Istvan Albert]

it is not forward or reverse, it is read 1 and read 2, or first in pair and second in pair,

alas, calling them as forward and reverse is very common, even in training materials ... so I understand why call them that way

forward and reverse represents the orientation of the alignment; either pair may align forward or reverse - read1 and read 2 indicate which file the reads come from. Using:

samtools flags 

will list the flag meaning:

   0x1     1  PAIRED         paired-end / multiple-segment sequencing technology
   0x2     2  PROPER_PAIR    each segment properly aligned according to aligner
   0x4     4  UNMAP          segment unmapped
   0x8     8  MUNMAP         next segment in the template unmapped
  0x10    16  REVERSE        SEQ is reverse complemented
  0x20    32  MREVERSE       SEQ of next segment in template is rev.complemented
  0x40    64  READ1          the first segment in the template
  0x80   128  READ2          the last segment in the template
 0x100   256  SECONDARY      secondary alignment
 0x200   512  QCFAIL         not passing quality controls or other filters
 0x400  1024  DUP            PCR or optical duplicate
 0x800  2048  SUPPLEMENTARY  supplementary alignment

you can see that 64 and 128 are READ1 and READ2