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Full Discussion: Diff command on two Fastq.gz files
Top Forums UNIX for Dummies Questions & Answers Diff command on two Fastq.gz files Post 302876830 by arcolombo698 on Tuesday 26th of November 2013 06:48:28 PM
Old 11-26-2013
Diff command on two Fastq.gz files
Hello.

I have to compare two different fastq.gz files that I concatenated, and then zipped into a new merge fastq.gz file.

The files that need to be merged are:
Sample-136-P_S7_L001_R1_001.fastq.gz and Sample -136-P_S7_L002_R1_001.fastq.gz

They were meged to a new file called:
Sample-136-P_S7_R1.fastq.gz

The command entered in Linux was (And this was completed successfully)
Code:
 zcat CHLA-136-P_S7_L001_R1_001.fastq.gz CHLA-136-P_S7_L002_R1_001.fastq.gz | gzip > CHLA-136-P_S7_R1.fastq.gz



Now I want to use the diff command to compare the two separate files with the combined file to measure any errors within the merge.

Command:
Code:
diff <(zcat CHLA-136-P_S7_L001_R1_001.fastq.gz CHLA-136-P_S7_L002_R1_001.fastq.gz) <(zcat CHLA-136-P_S7_R1.fastq.gz)


however this gives me the error ::: "Missing name for redirect".

How can I use the diff command on these two separate files with the concatenated file ?

Thank you!!
Last edited by Don Cragun; 11-26-2013 at 09:55 PM.. Reason: Add CODE and ICODE tags.
 

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LEARN ABOUT DEBIAN

ppmimgvquant

PPMIMGVQUANT(1) 					      General Commands Manual						   PPMIMGVQUANT(1)

NAME

       ppmimgvquant - palette quantifier for Pilot Image Viewer pgm files, version 2.0.

SYNOPSIS

       ppmimgvquant [-4] [-h] [-v] [ppmquant options]

DESCRIPTION

       ppmimgvquant just calls ppmquant(1) with the following map file:
	    P3
	    4 1
	    255
	      0   0   0
	     85  85  85
	    170 170 170
	    255 255 255
       If you specify -4, then we use this map file:
	    P3
	    16 1
	    255
	      0   0   0
	     17  17  17
	     34  34  34
	     51  51  51
	     68  68  68
	     85  85  85
	    102 102 102
	    119 119 119
	    136 136 136
	    153 153 153
	    170 170 170
	    187 187 187
	    204 204 204
	    221 221 221
	    238 238 238
	    255 255 255
       The ppmquant(1) output is also passed through ppmtopgm(1) to ensure a graymap output file.

OPTIONS

       -4     Convert to 4 depth image (for Palm IIIx/V).

       -h     Display a usage message and exit.

       -v     Display the version number and exit.

       All other switches are passed to ppmquant(1).

SEE ALSO

       imgvinfo(1), imgvtopnm(1), imgvview(1), pbmtoimgv(1), pgmtoimgv(1), ppmquant(1), ppmtopgm(1), pbm(5), pgm(5).

BUGS

       Bug reports should be sent to Eric A. Howe (mu@trends.net).

LICENSE

       Copyright (C) 1997,1998 Eric A. Howe <http://www.trends.net/~mu>.

       This  program  is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by
       the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

       This program is distributed in the hope that it will be useful, but WITHOUT ANY	WARRANTY;  without  even  the  implied	warranty  of  MER-
       CHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.

       You  should  have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation,
       Inc., 675 Mass Ave, Cambridge, MA 02139, USA.

								     Sept 1997							   PPMIMGVQUANT(1)
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