I am trying to use segemehl for reference assembly for the first time and compare the result to bowtie2. I noticed segemehl mapping quality output is 255, which as I understand means there isn't one provided. Is there a reason for this? I am using fastq file (I will provide the conditions below) so quality scores should be present and couldn't find anything on their manual regarding mapping quality information.
Input: segemehl_0_2_0/segemehl/segemehl.x -t 4 -d C_albicans_SC5314_A21_current_chromosomes.fasta -i C_albicans_SC5314_A21_current_chromosomes.idx -q CaLC-5-0-1-1_S4_L001_R1_001.fastq -p CaLC-5-0-1-1_S4_L001_R2_001.fastq > CaLC-5.sam
Line 12 of CaLC-5.sam (col. 5 for MAPQ, bolded): M03509:26:000000000-AUETC:1:1108:16923:2565 1:N:0:GCTACGCT+CTCTCTAT 99 Ca21chrR_C_albicans_SC5314 523171 255 251M = 523399 479 CTTCGAGGAAGAAATAAACAAAATAGGAGGAGACAGCGAAGATAGAACAAAGTCTGAAATTCCTTTTTTTTTTTCTTACTAGTAGGTAGTAAGGAGTAACCGTAACTAAAAATAATCGAGTCATTCTAATTTATCAACTGATAATGGTTCCAGTTACGTTTTCATTAGTTGAATGAAATAGAAACCAAATAGAAAATATTCAAACAGAATTGTATGATCTGTCATTTAATAGTGGTTATATATATATTATA CCCCC@FBCFFFGGGGGGGGGGHHHHHHHGGGHGHHHGGGGGHHHHHHHHHHGHHHHHHHHHHHHHHHGGGGGGGHHHHHHHGHHHFGH3FHHHEHHHHGHGGHGGHHHHHHHHHHHGHGHHHHHGHHHHHHHHHHHHHHHHHHHGHHHHGHHHHHHGHHHGHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHGHGHHHHGGGFGGGBFFGGGGGGGGBFBCBFFFGGFGFGGGGGGFGEGB NM:i:0 MD:Z:251 NH:i:1 XI:i:0 XA:Z:P
This is the first time posting on biostars forum so please let me know if you'd like more clarifications.
Thanks!
David
