Hi ,
I have a typical situation. I have 4 files and with different headers (number of headers is varible ).
I need to make such a merged file which will have headers combined from all files (comman coluns should appear once only).
For example -
File 1
H1|H2|H3|H4
11|12|13|14
21|22|23|23... (1 Reply)
Hello,
A bioperl problem I thought could be done with awk: convert the fasta format (Note: the length of each row is not the same for each entry as they were combined from different files!) to tabular format.
input.fasta:
>YAL069W-1.334 Putative promoter sequence... (6 Replies)
Hi
I have an alignment file (.fasta) with ~80 sequences. They look like this-
>JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0
GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT
TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)
Hi,
I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help .
input
> fefrwefrwef X900
AGAGGGAATTGG
AGGGGCCTGGAG
GGTTCTCTTC
> fefrwefrwef X932
AGAGGGAATTGG
AGGAGGTGGAG
GGTTCTCTTC
> fefrwefrwef X937... (2 Replies)
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Hi. Unix rookie here. Been looking for a few days for reference documents on how BSD UNIX lays the logical file format onto a disk. Goal is to view/edit with hex editor for data repair. Lots of docs are available for how to use Unix commands (like xxd), but I want to learn the map of how Unix... (4 Replies)
I have the following script:
awk 'FNR==NR{s+=$3;next;} { print $1 , $2, 100*$3/s }'
and the following file:
>P39PT-1224 Freq 900
cccctacgacggcattggtaatggctcagctgctccggatcccgcaagccatcttggatatgagggttcgtcggcctcttcagccaagg-cccccagcagaacatccagctgatcg
>P39PT-784 Freq 2... (2 Replies)
I would like to extract all entries containing the following patterns: ccccta & ccccccccc from the following infile:
>P39PT-1224_Freq_900
cccctacgacggcattggtaatggctcccgcaagccatctctcttcagccaagg
>P39PT-784_Freq_2
cccctacgacggcattggtaatggcacccgcaagccatctctcttccccccccc
>P39PT-678_Freq_5... (4 Replies)
I have two fasta files as shown below,
File:1
>Contig_1:90600-91187
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG
>Contig_24:26615-28387... (11 Replies)
I have 5 sequences in a fasta file namely gene1.fasta as follows,
gene1.fasta
>1256
ATGTAGC
>GEP
TAGAG
>GTY578
ATGCATA
>67_iga
ATGCTGA
>90_ld
ATGCTG
I need to rename the gene1.fasta file based on the sequence position specified in list.txt as follows,
list.txt
position1=org5... (5 Replies)
Discussion started by: dineshkumarsrk
5 Replies
LEARN ABOUT DEBIAN
ampliconnoise
AMPLICONNOISE(1) AmpliconNoise Documentation AMPLICONNOISE(1)NAME
AmpliconNoise - remove noise from high throughput nucleotide sequence data
VERSION
This documentation refers to version 1.22
SYNOPSIS
See /usr/share/doc/ampliconnoise/Doc.pdf.gz for details of how to run.
DESCRIPTION
The following tools are included. Most of them have an MPI equivalent, for example SeqNoise has an equivalent SeqNoiseM which can be used
with mpirun.
FastaUnique - dereplicates fasta file
-in string input file name
Options:
FCluster
-in string distance input file name
-out string output file stub
Options:
-r resolution
-a average linkage
-w use weights
-i read identifiers
-s scale dist.
NDist - pairwise Needleman-Wunsch sequence distance matrix from a fasta file
-in string fata file name
Options:
-i output identifiers
Perseus - slays monsters
-sin string seq file name
Options:
-tin string reference sequence file
-a output alignments
-d use imbalance
-rin string lookup file name
PyroDist - pairwise distance matrix from flowgrams
-in string flow file name
-out stub out file stub
Options:
-ni no index in dat file
-rin string lookup file name
PyroNoise - clusters flowgrams without alignments
-din string flow file name
-out string cluster input file name
-lin string list file
Options:
-v verbose
-c double initial cut-off
-ni no index in dat file
-s double precision
-rin file lookup file name
SeqDist - pairwise distance matrix from a fasta file
-in string fasta file name
Options:
-i output identifiers
-rin string lookup file name
SeqNoise - clusters sequences
-in string sequence file name
-din string distance matrix file name
-out string cluster input file name
-lin string list file
Options:
-min mapping file
-v verbose
-c double initial cut-off
-s double precision
-rin string lookup file name
SplitClusterEven
-din string dat filename
-min string map filename
-tin string tree filename
-s split size
-m min size
AUTHOR
All software by Chris Quince (quince@civil.gla.ac.uk) This manpage by Tim Booth (tbooth@ceh.ac.uk)
LICENCE AND COPYRIGHT
Copyright (c) 2009 (quince@civil.gla.ac.uk). All rights reserved.
Released under the Lesser GPL.
Permission is granted for anyone to copy, use, or modify these programs and documents for purposes of research or education, provided this
copyright notice is retained, and note is made of any changes that have been made.
perl v5.12.4 2011-04-28 AMPLICONNOISE(1)