It did not work. When I run sff extract I get something like file.MID38.fastq which is why I think it did not work, at first I was getting an error saying that it was not a directory. I removed the
and I did not get any error but it still did not change the fastq to a fasta.
Last edited by jrymer; 08-06-2012 at 03:01 PM..
Reason: forgot code tags
Hi,
I have a program that runs two threads in stead of two processes. I want to use pipe to redirect the output of the first thread to the input of the second thread.
One thread is continuously writing to a pipe, and the other thread will read from the pipe.
How do I do that?
Is there... (2 Replies)
i am new to linux programming. can anyone answer my question?
there is one pipe file "my_pipe"
prw-r--r-- 1 john rnd 32 Aug 17 19:45 my_pipe
how to output string message (char*) to this pipe? which API should I use? (3 Replies)
anybody can help, plz:
I want to pass the output of "ls" to "grep":
ftp -n host <<!
USER user passwd
ls
bye
! | grep file
exit 0
It does not work!!
Any idea??
Sami (7 Replies)
I am using grep and I want the output to go into two files without going to the screen. I used tee to get the output into two files, but it is also putting the output on the screen which i do not want. Can this be fixed. (2 Replies)
Hi,
I am having a list of directories with different login id's. My requirement is that i need to list the directories of my id and need to delete them. So i am using following code
ls -ltr ¦ grep userid ¦ rm -rf
But this is not working. So is there any way of doing it. Please note... (3 Replies)
Hi All. Thanks for your help in advance.
I have a requirement to examine the number of delimiters in each record of a file. If the record has the expected number of delimiters it should be passed into a 'good' file. If it does not, the record should be passed into a 'bad' file. I have been able... (8 Replies)
I can use pipe output to a file. For example
./somescript.sh > output.txt
But for example if the output from ./somescript.sh is slow. like if it prints one line every minute then output.txt is not updated every minute. Lines are written to output.txt in one go, hence have to wait for the whole... (2 Replies)
Hi All,
i have the following command
df|awk '{print $5}'|grep /| egrep -v '^/$|/usr|/opt|/var/log|/home|/tmp'
output looks like:
/filesystem/number1
/filesystem/number2
/filesystem3
/possiblymoreoutput
i want the output to look like the below (either in a file or to output to... (3 Replies)
I'm trying to get an output to echo on the next line in a given color and outputted next to a label.
Sorry if that's a bit vague, see below.
#!/bin/bash
YELLOW=$(tput setaf 3 && tput bold)
echo -n 'plaintext' | openssl md2 || read hash
echo "$YELLOW Hash:$hash"
But I can't seem to get the... (2 Replies)
Hi,
I want to grep multiple patterns from multiple files and save to multiple outputs. As of now its outputting all to the same file when I use this command.
Input : 108 files to check for 390 patterns to check for. output I need to 108 files with the searched patterns.
Xargs -I {} grep... (3 Replies)
Discussion started by: Diya123
3 Replies
LEARN ABOUT DEBIAN
srf2fastq
srf2fastq(1) Staden io_lib srf2fastq(1)NAME
srf2fastq - Converts SRF files to Sanger fastq format
SYNOPSIS
srf2fastq [options] srf_archive ...
DESCRIPTION
srf2fastq extracts sequences and qualities from one or more SRF archives and writes them in Sanger fastq format to stdout.
Note that Illumina also have a fastq format (used in the GERALD directories) which differs slightly in the use of log-odds scores for the
quality values. The format described here is using the traditional Phred style of quality encoding.
OPTIONS -c Outputs calibrated confidence values using the ZTR CNF1 chunk type for a single quality per base. Without this use the original
Illumina _prb.txt files consisting of four quality values per base, stored in the ZTR CNF4 chunks.
-C Masks out sequences tagged as bad quality.
-s root
Generates files on disk with filenames starting root, one file per non-explicit element in the SRF/ZTR region (REGN) chunk. Typi-
cally this results in two files for paired end runs. The filename suffixes come from the names listed in the SRF region chunks.
This option conflicts with the -S parameter.
-S Splits sequences into regions, but sequentially lists each sequence region to stdout instead of splitting to separate files on disk.
This option conflicts with the -s parameter.
-n When using -s the filename suffixes are simply numbered (starting with 1) instead of using the names listed in the SRF region
chunks.
-a Appends region index to the sequence names. Ie generate "name/1" and "name/2" for a paired read.
-e Include any explicit sequence (ZTR region chunk of type 'E') in the sequence output. The explicit sequence is also included in the
quality line too. Currently this is utilised by ABI SOLiD to store the last base of the primer.
-r region list
Reverse complements the sequence and reverses the quality values for all regions in the region list. This is a comma separated list
of integer values enumerating the regions, starting from 1. Note that this option only works when either -s or -S are specified.
EXAMPLES
To extract only the good quality sequences from all srf files in the current directory using calibrated confidence values (if available).
srf2fastq -c -C *.srf > runX.fastq
To extract a paired end run into two separate files with sequences named name/1 and name/2.
srf2fastq -s runX -a -n runX.srf
To extract a paired end run as a single file, alternating forward and reverse sequences, with the second read being reverse complemented.
srf2fastq -S -r 2 runX.srf > runX.fastq
AUTHOR
James Bonfield, Steven Leonard - Wellcome Trust Sanger Institute
December 10 srf2fastq(1)