03-10-2014
[Solved] Count and search by sequence in multiple fasta file
Hello,
I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long unique reads. Now i wanted to count each unique read appearance in all the fasta files and make a table with sample names as columns and reads as rows. I tried to use "grep -w "sequence name" file name " to count the tags but this seems to take long time. does anyone know how to do this faster?
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LEARN ABOUT DEBIAN
srf_info
srf_info(1) Staden io_lib srf_info(1)
NAME
srf_info - Lists information about the contents of an SRF file
SYNOPSIS
srf_info [-l bitmap] srf_archive ...
DESCRIPTION
srf_info lists some simple frequency metrics on the contents of an SRF file, both in terms of how many traces there are and the sort of
data held within them.
For efficiencies sake some control is given over which statistics to gather and display. This is controlled by the -l level parameter. The
value is the summation of one or more of the following values, representing the data to display.
1 Count of good/bad reads.
2 Counts and compressed size for selected chunk types.
4 Trace count and trace name prefix for each trace_header.
8 Base count.
OPTIONS
-l bitmap
Controls which statistics to gather and display. Bitmap is a value from 0 to 15 (1+2+4+8) as described in the DESCRIPTION section
above.
EXAMPLES
To count the total number of good and bad reads along with a break down of trace names per SRF data-block-header we would use bitmap values
1 and 4 combined.
srf_info -l 5 foo.srf
To count the total number of reads for all srf files in a directory.
srf_info -l 1 *.srf
AUTHOR
Steven Leonard, Wellcome Trust Sanger Institute
September 19 srf_info(1)