Can bowtie2 mapping paired-end reads of different length?

Question

[whiteeagle115]

Hello!

I began to analyze some reads of a genome of a haploid organisms. The genome was made with HiSeq and during trimerization, the adapters were removed and this generated reads of different sizes in the paired-end files.

I used the following command:

bowtie2 -x SalI -1 121_MSO.Adtrim_1.fastq -2 121_MSO.Adtrim_2.fastq -p 20 -D 20 -R 3 -N 1 -L 20 -i S,1,0.5 -S 1_21.sam

When I try to rotate the bowtie it generates the following error:

Warning: skipping mate #2 of read 'MG00HS19:1041:CBBT1ANXX:1:1101:11867:2106 2:N:0:GAGTGG' because length (1) <= # seed mismatches (1)
Warning: skipping mate #2 of read 'MG00HS19:1041:CBBT1ANXX:1:1101:11867:2106 2:N:0:GAGTGG' because it was < 2 characters long
Warning: skipping mate #2 of read 'MG00HS19:1041:CBBT1ANXX:1:1101:14352:2179 2:N:0:GAGTGG' because length (1) <= # seed mismatches (1)
Warning: skipping mate #2 of read 'MG00HS19:1041:CBBT1ANXX:1:1101:14352:2179 2:N:0:GAGTGG' because it was < 2 characters long
Warning: skipping mate #2 of read 'MG00HS19:1041:CBBT1ANXX:1:1101:15207:2236 2:N:0:GAGTGG' because length (1) <= # seed mismatches (1)
Warning: skipping mate #2 of read 'MG00HS19:1041:CBBT1ANXX:1:1101:15207:2236 2:N

Thanks for all!

[GouthamAtla]

It says that the reads are too short to align. When you trim the data, try to remove reads are less than 20bp long, as your -L is 20

[whiteeagle115]

Thanks! I will see that!

Answer 1

[Bioaln]

From documentation, the -L parameter dictates the lower seed length bound. This is according to warnings the problem (as noted by @geek_y)