I tried to align fastq-files with BS-Seeker3 but no 1 read was mapped.
$ ./bs3-align -1 B213-036-pool_S6_L001_R1_001.fastq -2 B213-036-pool_S6_L001_R2_001.fastq -o B213-036 -f sam -g reference_genome/genome.fa -d reference_genome/
BS-Seeker3 beta
Welcome to SNAP version 1.0.0.
Loading index from directory... 0s. 60856842 bases, seed size 20
Aligning.
Total Reads Aligned, MAPQ >= 10 Aligned, MAPQ < 10 Unaligned Too Short/Too Many Ns %Pairs Reads/s Time in Aligner (s)
398,926 0 (0.00%) 0 (0.00%) 398,926 (100.00%) 0 (0.00%) 0.00% 60,979 7
(None, None)
BS-seeker3 Result
Final Alignment Report
================================================
Number of reads in total: 398926
Number of unique-hits reads (before post-filtering): 0.0
Number of reads mapped after post-filtering 0.0
Alignment Time: 9.74573802948secs
Final Cytosine Report
================================================
Total Number of Cytosines: 0.0
Total Number of Cs in CpG context: 0.0
Total Number of Cs in CHG context: 0.0
Total Number of Cs in CHH context: 0.0
Rate of Methylation
mCG 0.000%
mCHG 0.000%
mCHH 0.000%
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I tried to align fastq-files with BS-Seeker3 but no 1 read was mapped.