Hi,
I am using MACS2 for ChIP-seq peak calling.
I have a treatment file with original reads of 51bp. Before alignment, the reads were dynamically trimmed on 3'end for removing low quality bases (with Trimmomatic software). At the end, aligned reads ranges from 42 to 51 bp.
Then, I have a control (input) file with original reads of 36 bp. Before alignment, the reads were dynamically trimmed on 3'end for removing low quality bases (with Trimmomatic software). At the end, aligned reads ranges from 30 to 36 bp.
If I let MACS to automatically determine the tags size, MACS comes out with a wrong number. Moreover, since I think MACS scan only the first n reads, MACS does not give the average of the tags length.
So, I have to specify the tag size with the option --tsize. However, it is impossible to set a tsize for the treatment and a different tsize for the input.
What do you think is the best solution for this situation?
Thanks very much!
Albert
I am using MACS2 for ChIP-seq peak calling.
I have a treatment file with original reads of 51bp. Before alignment, the reads were dynamically trimmed on 3'end for removing low quality bases (with Trimmomatic software). At the end, aligned reads ranges from 42 to 51 bp.
Then, I have a control (input) file with original reads of 36 bp. Before alignment, the reads were dynamically trimmed on 3'end for removing low quality bases (with Trimmomatic software). At the end, aligned reads ranges from 30 to 36 bp.
If I let MACS to automatically determine the tags size, MACS comes out with a wrong number. Moreover, since I think MACS scan only the first n reads, MACS does not give the average of the tags length.
So, I have to specify the tag size with the option --tsize. However, it is impossible to set a tsize for the treatment and a different tsize for the input.
What do you think is the best solution for this situation?
Thanks very much!
Albert
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