MeRIPPeR/config.xml at master · cmason-lab/MeRIPPeR · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
<meripper>
	<data>
		<samples>
			<sample name="Huh7">
				<replicate name="7">
					<ip>Huh7_HCV_m6A</ip>
					<control>Huh7_HCV_Flag</control>
				</replicate>
			</sample>
			<sample name="Huh7_5">
				<replicate name="7_5">
					<ip>Huh7_5_HCV_m6A</ip>
					<control>Huh7_5_HCV_Flag</control>
				</replicate>
			</sample>
		</samples>
	</data>
	<configuration>
		<aligner>star</aligner>
		<num_threads>5</num_threads>
		<genome>HCV</genome>
		<genome_fa>hcv_genome/HCV.fasta</genome_fa>
		<genome_fai>hcv_genome/HCV.fasta.fai</genome_fai>
		<genome_dir>hcv_genome/</genome_dir>
		<tophat_genome_dir>hcv_genome/bowtie2/hcv</tophat_genome_dir>
		<bwa_index>hcv_genome/bwa/HCV.fasta</bwa_index>
		<gsnap_genome_dir>/zenodotus/dat01/mason_lab_scratch_reference/cmlab/GENOMES/GMAPDB</gsnap_genome_dir>
		<gsnap_iit>-s /zenodotus/dat01/mason_lab_scratch_reference/cmlab/GENOMES/GMAPDB/hg19/hg19.maps/hg19.refseq.splicesites.iit</gsnap_iit>
		<refseq_dir>/home/yos2006/refseq</refseq_dir>
		<genome_sizes>hcv_genome/hcv.sizes</genome_sizes>
		<mapping_quality_threshold>20</mapping_quality_threshold>
		<window_size>25</window_size>
		<window_min_size>100</window_min_size>
		<window_max_size>200</window_max_size>
		<alpha>0.05</alpha>
		<star_index>hcv_genome/star/</star_index>
		<star_load> --genomeDir hcv_genome/star/ --genomeLoad LoadAndExit --outFileNamePrefix star_genome_load</star_load>
		<star_remove> --genomeDir hcv_genome/star/ --genomeLoad Remove --outFileNamePrefix star_genome_remove</star_remove>
	</configuration>
</meripper>