Dear All,
I am trying to figure out how to set a mismatch (--score-min) value in Bowtie2. On the forum I have seen '--score-min' settings like 'L, -0.5,-0.2', 'C,0,0', 'C,-1,0' and the assigned default setting by Bowtie2 is 'L,-0.6,-0.6'.
I wish to know the reasons behind deciding values for '--score-min' option. Bowtie2 manual mentions some details that it is a function of read length etc. but does not divulge into further details on how does one decide which function to choose as both 'L' (Linear) and 'C' (Constant) have been used in the cases mentioned above as well as the rationale behind the other two parameters.
My dataset is from Illumina Hi-Seq 2500 and reads are 150 bp long. I want to try a range of mismatch settings from 1 to 11 or so with '--very-sensitive' option under the '--end-to-end' mode.
I would highly appreciate any feedback on this.
Regards,
Sanjeevksh
I am trying to figure out how to set a mismatch (--score-min) value in Bowtie2. On the forum I have seen '--score-min' settings like 'L, -0.5,-0.2', 'C,0,0', 'C,-1,0' and the assigned default setting by Bowtie2 is 'L,-0.6,-0.6'.
I wish to know the reasons behind deciding values for '--score-min' option. Bowtie2 manual mentions some details that it is a function of read length etc. but does not divulge into further details on how does one decide which function to choose as both 'L' (Linear) and 'C' (Constant) have been used in the cases mentioned above as well as the rationale behind the other two parameters.
My dataset is from Illumina Hi-Seq 2500 and reads are 150 bp long. I want to try a range of mismatch settings from 1 to 11 or so with '--very-sensitive' option under the '--end-to-end' mode.
I would highly appreciate any feedback on this.
Regards,
Sanjeevksh
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