Hi,
My question concerns Bowtie's –e (--maqerr) parameter.
If I understand correctly, while –n sets the maximum number of mismatches permitted in the "seed", the total number of mismatches over the entire read length can be controlled by the –e parameter. Indeed, increasing this parameter could greatly increase the number of aligned reads. For example, in one sample that I tested, increasing –e from 70 (default) to 140, increased the percentage of aligned reads from 31% to 48%.
Default (-e 70)
--------------------------------
# reads processed: 4424341
# reads with at least one reported alignment: 1395000 (31.53%)
# reads that failed to align: 3029341 (68.47%)
-e 140
--------------
# reads processed: 4424341
# reads with at least one reported alignment: 2125127 (48.03%)
# reads that failed to align: 2299214 (51.97%)
Does the default value (70) is the recommended level for 36 bp reads? Did anyone test how –e should be increased with the increasing of reads length? For example, any recommendation on how –e should be increased if reads length is 80 bp?
Many thanks in advance,
Rani
My question concerns Bowtie's –e (--maqerr) parameter.
If I understand correctly, while –n sets the maximum number of mismatches permitted in the "seed", the total number of mismatches over the entire read length can be controlled by the –e parameter. Indeed, increasing this parameter could greatly increase the number of aligned reads. For example, in one sample that I tested, increasing –e from 70 (default) to 140, increased the percentage of aligned reads from 31% to 48%.
Default (-e 70)
--------------------------------
# reads processed: 4424341
# reads with at least one reported alignment: 1395000 (31.53%)
# reads that failed to align: 3029341 (68.47%)
-e 140
--------------
# reads processed: 4424341
# reads with at least one reported alignment: 2125127 (48.03%)
# reads that failed to align: 2299214 (51.97%)
Does the default value (70) is the recommended level for 36 bp reads? Did anyone test how –e should be increased with the increasing of reads length? For example, any recommendation on how –e should be increased if reads length is 80 bp?
Many thanks in advance,
Rani
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