Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Combining 3 fastq files
Top Forums Shell Programming and Scripting Combining 3 fastq files Post 302730723 by ljk on Tuesday 13th of November 2012 01:43:38 PM
Old 11-13-2012
Combining 3 fastq files
Hello,
I am working with next-gen short-read sequence data, which we receive in 3 fastq files. These are arranged in 4-line groups for each read:
line1: read identifier, beginning, e.g., "@HWI-ST1342..."
line2: DNA sequence, for files 1 and 2, 101 characters, for file 3, 7 chars.
line3: "+"
line4: quality score codes equaling line 2 in length.

There are ~160 million reads in total per file, so quite big files.

I need to compile the data from all three files, which are in the same order and have the same read identifier between the files. So what I need to do is:

line1: identifier
line2: File1sequenceFile2sequenceFile3sequence
line3: "+"
line4: File1qualFile2qualFile3qual

Can anyone suggest an efficient way of doing this with shell commands?

thanks a lot!
 

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

combining files

how will i combine these 2 files below, with the desired output specified below: file1: one two three four file2: red blue yellow green file3: aaa bbb ccc ddd (3 Replies)
Discussion started by: apalex
3 Replies

2. UNIX for Dummies Questions & Answers

Combining files

Hi, is there a way to combine 2 files together, joining line 1 from file A with line 1 from file B, line 2 from A with line 2 from B etc. File A File B 1 4 2 5 3 6 Combined result = File C 14 25 36 (2 Replies)
Discussion started by: Enda Martin
2 Replies

3. Shell Programming and Scripting

Combining Two Files

I have two files which contain data from two different transactions in the same format: <Name> - <Count> My goal is to end up with data in this format after combining the two: <Name> - <Count1> - <Count2> Is this possible to do with awk, or is there something better? Thanks... (3 Replies)
Discussion started by: bat711
3 Replies

4. Shell Programming and Scripting

Combining Two Files

Could someone help me reduce the number of runs for a shell program I created? I have two text files below: $ more list1.txt 01 AAA 02 BBB 03 CCC 04 DDD $ more list2.txt 01 EEE 02 FFF 03 GGG I want to combine the lines with the same number to get the below: 01 AAA 01 EEE 02... (4 Replies)
Discussion started by: stevefox
4 Replies

5. UNIX for Dummies Questions & Answers

combining two files

Hi Gurus, I have 2 files: File1 Filename1 xx Filename1 yy Filename1 Total Filename2 xx Filename2 yy Filename2 zz Filename2 Total Filename3 xx Filename3 Total and File2: Filename1 10296 xxx Date: 09/01/08 Filename2 10296 xxx Date: 09/05/08... (36 Replies)
Discussion started by: rock1
36 Replies

6. UNIX for Dummies Questions & Answers

Need Help in reading N days files from a Directory & combining the files

Hi All, Request your expertise in tackling one requirement in my project,(i dont have much expertise in Shell Scripting). The requirement is as below, 1) We store the last run date of a process in a file. When the batch run the next time, it should read this file, get the last run date from... (1 Reply)
Discussion started by: dsfreddie
1 Replies

7. Shell Programming and Scripting

Combining 2 files

i am having 2 files like this file 1 1, 2, 3, 4, file2 5, 6, 7, 8, what i want do is like this i want to put all the contents for file 2 after file 1,means adding column in file1 (5 Replies)
Discussion started by: sagar_1986
5 Replies

8. Shell Programming and Scripting

Combining files

Hi I have about 108 files (text files) that end with .avg and each one of these files have a distinct name that describes what is in the file. In each file there is a set of 80 values that are tab separated. I want to combine all 108 files into ONE main file. So each file is named: 1.avg... (5 Replies)
Discussion started by: phil_heath
5 Replies

9. UNIX for Dummies Questions & Answers

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:... (1 Reply)
Discussion started by: arcolombo698
1 Replies

10. UNIX for Beginners Questions & Answers

Comparing fastq files and outputting common records

I have two files: File_1: @M04961:22:000000000-B5VGJ:1:1101:9280:7106 1:N:0:86 GGCATGAAAACATACAAACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAATACCATGAAAAATATCAACCACACCAGAAGCAGCAT + GGGGGGGGGGGGGGGGGCCGGGGGF,EDFFGEDFG,@DGGCGGEGGG7DCGGGF68CGFFFGGGG@CGDGFFDFEFEFF:30CGAFFDFEFF8CAF;;8F ... (3 Replies)
Discussion started by: Xterra
3 Replies

LEARN ABOUT OSF1

cam

cam(1)                                                        General Commands Manual                                                       cam(1)

NAME

       cam - CPU'S AUDIO MIXER for Linux

SYNOPSIS

       cam    [-v  x,y]  [--volume  x,y]  [-b  x,y]  [--bass  x,y]  [-t  x,y]  [--treble x,y] [-s x,y] [--synth x,y] [-p x,y] [--pcm x,y] [-S x,y]
              [--speaker x,y] [-l x,y] [--line x,y] [-m x,y] [--mic x,y] [-c x,y] [--cd x,y] [-M x,y] [--mixer x,y] [-a x,y]  [--altpcm  x,y]  [-r
              x,y] [--reclev x,y] [-i x,y] [--igain x,y] [-o x,y] [--ogain x,y] [-l1 x,y] [--line1 x,y] [-l2 x,y] [--line2 x,y] [-l3 x,y] [--line3
              x,y] [-3d 1|0] [--3dse 1|0] [-agc 1|0] [--agc 1|0] [-h] [-?] [--help] [-get] [-save] [-getfile filename] [-savefile filename]

       xcam

DESCRIPTION

       This is an audio mixer for Linux. You have the choice to use it with an interface or at the command line.

OPTIONS

       When using the interface you can use the following keys :

       LEFT ARROW
              decrease the volume of the current device.

       RIGHT ARROW
              increase the volume of the current device.

       UP ARROW
              go to previous device.

       DOWN ARROW
              go to next device.

       L      locks or unlocks :
              unlocked : you can control the left and right channel
              separately.
              lock : left and right channel are controlled together.

       R      turn on/off recording mode :
              red lamp : recording turned on
              green lamp : recording turned off

       3      turn on/off 3D Stereo Enhancement (3DSE) device :
              when turned on green indicator 3D will be lit at the left side of main volume handle.

       A      turn on/off microphone Automatic Gain Control :
              when turned on green indicator AGC will be lit at the left side of microphone volume handle.

       S      save the settings of ALL devices in a file ($HOME/.camrc)

       G      loads the saved settings and restores them.

       H      shows the help screen.

       Q/ESC  exits the program and returns to shell.

       NOTE: you can use upper or lower case.

       When using the command line options the interface is not shown.

       The following options are available :

       -v, --volume x,y
                 Set 'volume' to x (left) and y (right)

       -b, --bass x,y
                 Set 'bass' to x (left) and y (right)

       -t, --trebble x,y
                 Set 'treble' to x (left) and y (right)

       -s, --synth x,y
                 Set 'synth' to x (left) and y (right)

       -p, --pcm x,y
                 Set 'pcm' to x (left) and y (right)

       -S, --speaker x,y
                 Set 'speaker' to x (left) and y (right)

       -l, --line x,y
                 Set 'line in' to x (left) and y (right)

       -m, --mic x,y
                 Set 'microphone' to x (left) and y (right)

       -c, --cd x,y
                 Set 'CD in' to x (left) and y (right)

       -I, --imix x,y
                 Set 'mixer' to x (left) and y (right)

       -a, --altpcm x,y
                 Set 'altpcm' to x (left) and y (right)

       -r, --reclev x,y
                 Set 'record level' to x (left) and y (right)

       -i, --igain x,y
                 Set 'input gain' to x (left) and y (right)

       -o, --ogain x,y
                 Set 'output gain' to x (left) and y (right)

       -l1, --line1 x,y
                 Set 'line 1' to x (left) and y (right)

       -l2, --line2 x,y
                 Set 'line 2' to x (left) and y (right)

       -l3, --line3 x,y
                 Set 'line 3' to x (left) and y (right)

       -3d, --3dse 1|0
                 Set 3D Stereo Enhancement to 1 (on) or 0 (off)

       -agc, --agc 1|0
                 Set Automatic Gain Control for microphone to 1 (on) or 0 (off)

       -get      restore the saved values from $HOME/.camrc

       -save     save the values to $HOME/.camrc

       -getfile filename
                 restore the saved values from file 'filename'

       -savefile filename
                 save the values to file 'filename'

       -h, -?, --help
                  displays help

       NOTE: x and y are in range from 1 to 100. Higher or lower numbers are
       ignored.

BUGS

       None known as yet.  If you find one, please let me know.

AUTHOR

       Jan 'TWP' VANDENBERGHE  <jvdbergh@uia.ua.ac.be>

                                                                                                                                            cam(1)
All times are GMT -4. The time now is 11:16 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy