Changes between Version 58 and Version 59 of SOPs/atac_Seq


Ignore:
Timestamp:
06/11/21 14:50:34 (4 years ago)
Author:
thiruvil
Comment:

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  • SOPs/atac_Seq

    v58 v59  
    190190 *  [[https://github.com/LiuLabUB/HMMRATAC | HMMRATAC]]
    191191 *  [[https://github.com/jsh58/Genrich | Genrich]]
    192  * Run MACS2 with BAMPE option for PE reads, i.e. -f BAMPE, this asks MACS pileup and infer the real fragment size from the alignment.  Note: this option can be used to find accessible regions but not suitable for finding exact cut sites.  Also, comparing this option with converting to BED format (above), the BAMPE peaks calls are more conservative and may miss real peaks.
     192 * Run MACS2 with BAMPE option for PE reads, i.e. -f BAMPE, this asks MACS to pileup and infer the real fragment size from the alignment.  Note: this option can be used to find accessible regions but not suitable for finding exact cut sites.  Also, comparing this option with converting to BED format (above), the BAMPE peaks calls are more conservative and may miss real peaks.
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