Thank you singh,
Your command prints all the sequences. However, I need to print only few sequences length as listed in id.txt file. If I did not understand your commands properly, please let me know, where to include id.txt file in your command?
Oh ok, I was in impression that you want to print all seq strings length in a single Input_file, could you please try following now.
Output will be as follows.
Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
I have a fastq file from small RNA sequencing with sequence lengths between 15 - 30. I wanted to filter sequence lengths between 21-25 and write to another fastq file. how can i do that? (4 Replies)
Hi,
I am having a file of dna sequences in fasta format which look like this:
>admin_1_45
atatagcaga
>admin_1_46
atatagcagaatatatat
with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to... (5 Replies)
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
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... (5 Replies)
I have a fasta file as follows
>sp|O15090|FABP4_HUMAN Fatty acid-binding protein, adipocyte OS=Homo sapiens GN=FABP4 PE=1 SV=3
MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKN
TEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVM
KGVTSTRVYERA
>sp|L18484|AP2A2_RAT AP-2... (3 Replies)
Hi
How can I extract sequences from a fasta file with respect a certain criteria? The beginning of my file (containing in total more than 1000 sequences) looks like this:
>H8V34IS02I59VP
SDACNDLTIALLQIAREVRVCNPTFSFRWHPQVKDEVMRECFDCIRQGLG
YPSMRNDPILIANCMNWHGHPLEEARQWVHQACMSPCPSTKHGFQPFRMA... (6 Replies)
Hi,
I have a fasta file with multiple sequences. How can i get only unique sequences from the file.
For example
my_file.fasta
>seq1
TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC
>seq2... (3 Replies)
I have this file:
>ID1
AA
>ID2
TTTTTT
>ID-3
AAAAAAAAA
>ID4
TTTTTTGGAGATCAGTAGCAGATGACAG-GGGGG-TGCACCCC
Add I am trying to use this script to output sequences longer than 15 characters:
sed -r '/^>/N;{/^.{,15}$/d}'
The desire output would be this:
>ID4... (8 Replies)
I have a fasta file as follows
>sp|Q8WWQ8|STAB2_HUMAN Stabilin-2 OS=Homo sapiens OX=9606 GN=STAB2 PE=1 SV=3
MMLQHLVIFCLGLVVQNFCSPAETTGQARRCDRKSLLTIRTECRSCALNLGVKCPDGYTM
ITSGSVGVRDCRYTFEVRTYSLSLPGCRHICRKDYLQPRCCPGRWGPDCIECPGGAGSPC
NGRGSCAEGMEGNGTCSCQEGFGGTACETCADDNLFGPSCSSVCNCVHGVCNSGLDGDGT... (3 Replies)
Hi,
I have to add 7 bases of specific nucleotide at the beginning and ending of all the fasta sequences of a file. For example, I have a multi fasta file namely test.fasta as given below
test.fasta
>TalAA18_Xoo_CIAT_NZ_CP033194.1:_2936369-2939570:+1... (1 Reply)
Discussion started by: dineshkumarsrk
1 Replies
LEARN ABOUT DEBIAN
nifti_stats
NIFTI_STATS(1) User Commands NIFTI_STATS(1)NAME
nifti_stats - compute NIfTI statistical functions
SYNOPSIS
nifti_stats [-q|-d|-1|-z] value CODE [p1 p2 p3]
DESCRIPTION
nifti_stats supports several distributions (normal, uniform, logistic, chi, etc.) and calculates density or cummulative distribution func-
tion (and many more). Values are printed to stdout and can be piped to other tools.
value can be a single number or in the form bot:top:step.
default ==> output p = Prob(statistic < val).
-q ==> output is 1-p.
-d ==> output is density.
-1 ==> output is x such that Prob(statistic < x) = val.
-z ==> output is z such that Normal cdf(z) = p(val).
-h ==> output is z such that 1/2-Normal cdf(z) = p(val).
Allowable CODEs:
CORREL, TTEST, FTEST, ZSCORE, CHISQ, BETA, BINOM, GAMMA, POISSON, NORMAL, FTEST_NONC, CHISQ_NONC, LOGISTIC, LAPLACE, UNIFORM, TTEST_NONC,
WEIBULL, CHI, INVGAUSS, EXTVAL, PVAL, LOGPVAL and LOG10PVAL
Following CODE are distributional parameters, as needed.
Results are written to stdout, 1 number per output line.
EXAMPLE
Piping output into AFNI program 1dplot:
nifti_stats -d 0:4:.001 INVGAUSS 1 3 | 1dplot -dx 0.001 -stdin
SEE ALSO libnifti(1), nifti_tool(1), nifti1_test(1).
Homepage: http://niftilib.sourceforge.net
AUTHOR
RW Cox - SSCC/NIMH/NIH/DHHS/USA/EARTH - March 2004
This manual page was written by Michael Hanke <michael.hanke@gmail.com>, for the Debian project (but may be used by others).
nifti_stats September 2007 NIFTI_STATS(1)