I recently followed the protocol of m6A sequencing which is published in 2013 (Dominissini, Dan, et al. "Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing." Nature protocols 8.1 (2013): 176-189.). And I got two problems. Those troubles are found in running macs. At first, according to above reference paper, they used "--to-small" parameter. However, in my case, my computer said there isn't such option called "--to-small". Next, if I typed like this "macs14 -t IP.sam -c Input.sam --name=m6A --format="SAM" --gsize=282000000 --tsize=36 --nomodel --shiftsize=50 -w -S 2 > macs.out &", then there are some errors found like as follows.
# ARGUMENTS LIST:
# name = m6A
# format = SAM
# ChIP-seq file = IP.sam
# control file = Input.sam
# effective genome size = 2.82e+08
# band width = 300
# model fold = 10,30
# pvalue cutoff = 1.00e-05
# Large dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
INFO @ Wed, 17 Aug 2016 10:26:59: #1 read tag files...
INFO @ Wed, 17 Aug 2016 10:26:59: #1 read treatment tags...
Traceback (most recent call last):
File "/usr/local/bin/macs14", line 366, in <module> main()
File "/usr/local/bin/macs14", line 60, in main (treat, control) = load_tag_files_options (options)
File "/usr/local/bin/macs14", line 335, in load_tag_files_options ttsize = tp.tsize()
File "/usr/local/lib/python2.7/dist-packages/MACS14/IO/Parser.py", line 647, in tsize (chromosome,fpos,strand) = self.__fw_parse_line(thisline)
File "/usr/local/lib/python2.7/dist-packages/MACS14/IO/Parser.py", line 684, in __fw_parse_line bwflag = int(thisfields)
ValueError: invalid literal for int() with base 10: '-'
This is my first time to use macs, so if anyone helps me, I'll very appreciate it.