Skip to content

Commit

Permalink
Fix some typos in igvtools_readme, add samtools link
Browse files Browse the repository at this point in the history
  • Loading branch information
Jacob Silterra committed Feb 5, 2013
1 parent 1f4a26e commit d66a300
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions docs/igvtools_readme.txt
Original file line number Original file line Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ COMMANDS


The recognized commands are tile, count, sort, and index. Note that these The recognized commands are tile, count, sort, and index. Note that these
utilities are for working with ascii file formats, including SAM, but utilities are for working with ascii file formats, including SAM, but
do not work with BAM files. For manipulating BAM files use samtools. do not work with BAM files. For manipulating BAM files use samtools (http://samtools.sourceforge.net/).


--------------------------------------------------------------------------- ---------------------------------------------------------------------------
Command "tile" Command "tile"
Expand Down Expand Up @@ -144,7 +144,7 @@ Example:
Notes: Notes:


Data file formats, with the exception of .gct files, must be sorted by Data file formats, with the exception of .gct files, must be sorted by
start position. If neccessary files can be sorted with the "sort" command start position. If necessary files can be sorted with the "sort" command
described below. Attempting to preprocess an unsorted file will result described below. Attempting to preprocess an unsorted file will result
in an error. in an error.


Expand Down Expand Up @@ -201,7 +201,7 @@ Options:
--strands [arg] By default, counting is combined among both strands. --strands [arg] By default, counting is combined among both strands.
This setting outputs the count for each strand separately. This setting outputs the count for each strand separately.
Legal argument values are 'read' or 'first'. Legal argument values are 'read' or 'first'.
'read' Separates count by 'read' strand, 'first' uses the first in pair strand". 'read' Separates count by 'read' strand, 'first' uses the first in pair strand.
Results are saved in a separate column for .wig output, and a separate track Results are saved in a separate column for .wig output, and a separate track
for TDF output. for TDF output.


Expand Down

0 comments on commit d66a300

Please sign in to comment.