Converting .bowtie files to .sam

Question

[mmitra]

Hi all, I have a couple of .bowtie alignment files and I would like to convert them to .sam. Can anyone please suggest a way to do that? Thanks in advance!

[GenoMax]

There is no formal format called .bowtie. Are you sure these are not already in .sam format? What does file yourfile.bowtie show? Are you able see anything by head yourfile.bowtie?

[ATpoint]

OP probably means the default output of bowtie before it switched to SAM. There is this legacy script from an ancient samtools version that you can have a look at.

[mmitra]

Yes, it seems to be the default output of bowtie. I will check the legacy script.

[mmitra]

When I used the file command, I got "ASCII text". Here are first two lines of the file (used head command):

K00208:8:1101:273.14:91.19#0/1  -   chr3    185872452   CTTACATCCTAAAGAAAAAAAAGTAAATGTAAGACAACATAATAAAAGTTA L[e[LLVLL`VLV[LL[VL`Lii``e`e[Leii`Le`eeieiieieV[[LL 0   43:T>C

K00208:8:1101:281.26:91.19#0/1  +   chr15   76280494    CCCACATAGACGACTGATATAGCATGCTAATTGATCTCCCCATTACTATAC `[`ee[eeL[`L`VLVeie`[[LLLLHV[iVeL`L[LLLHHVLVL`LLLVL 0   5:C>A,23:C>A