To estimate conversion rates from our pyridine borane sequencing we created a spike-in of which 10% of all C's of a PCR fragment are fC's.
The length of the fragment is roughly 1.6 kb and we sequenced with PE150. In our test sequencing we have only ca. 250 spike-in reads per .bam file. I used astair align to align.
When using astair call -f /index_dir/spikein.fasta -i /input_dir/file_mCtoT.bam -d /output_dir/ it gives me the two expected files, however it says that there are 0 modified and 0 unmodified C's regardless of context.
By inspecting the bam files in IGV I can definitely confirm the alignment and as well the conversion, however, astair call just gives me the expected outputs with all zeros.
Do you have any clue what could be happening?
To estimate conversion rates from our pyridine borane sequencing we created a spike-in of which 10% of all C's of a PCR fragment are fC's.
The length of the fragment is roughly 1.6 kb and we sequenced with PE150. In our test sequencing we have only ca. 250 spike-in reads per .bam file. I used astair align to align.
When using
astair call -f /index_dir/spikein.fasta -i /input_dir/file_mCtoT.bam -d /output_dir/it gives me the two expected files, however it says that there are 0 modified and 0 unmodified C's regardless of context.By inspecting the bam files in IGV I can definitely confirm the alignment and as well the conversion, however, astair call just gives me the expected outputs with all zeros.
Do you have any clue what could be happening?