I could calculate the length of entire fasta sequences by following command,
But, I need to calculate the length of a particular fasta sequence specified/listed in another txt file. The results to to be printed in a csv file.
Therefore, please help me to do the same.
Thanks in advance.
Sorry mate without seeing sample of Input and expected output it is NOT possible to tweak a solution. So kindly do add sample of your Input_file(fasta file) and show us expected output file(.csv one) in CODE TAGS and let us know then.
Thanks,
R. Singh
These 2 Users 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
abacas
ABACAS(1) User Commands ABACAS(1)NAME
abacas - Algorithm Based Automatic Contiguation of Assembled Sequences
SYNOPSIS
abacas -r ref -q qs -p prog [OPTIONS]
OR
abacas -r ref -q psf -e
ref reference sequence in a single fasta file
qs contigs in multi-fasta format
rog MUMmer program to use: 'nucmer' or 'promer'
psf pseudomolecule/ordered sequence file in fasta format
OPTIONS
-h print usage
-d use default nucmer/promer parameters
-s int minimum length of exact matching word (nucmer default = 12, promer default = 4)
-m print ordered contigs to file in multifasta format
-b print contigs in bin to file
-N print a pseudomolecule without "N"s
-i int mimimum percent identity [default 40]
-v int mimimum contig coverage [default 40]
-V int minimum contig coverage difference [default 1]
-l int minimum contig length [default 1]
-t run tblastx on contigs that are not mapped
-g string (file name) print uncovered regions (gaps) on reference to file name
-a append contigs in bin to the pseudomolecule
-o prefix output files will have this prefix
-P pick primer sets to close gaps
-f int number of flanking bases on either side of a gap for primer design (default 350)
-R int Run mummer [default 1, use -R 0 to avoid running mummer]
-e Escape contig ordering i.e. go to primer design
-c Reference sequence is circular
DESCRIPTION
ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs
based on a reference sequence.
ABACAS uses MUMmer to find alignment positions and identify syntenies of assembled contigs against the reference. The output is then pro-
cessed to generate a pseudomolecule taking overlapping contigs and gaps in to account. ABACAS generates a comparision file that can be used
to visualize ordered and oriented contigs in ACT. Synteny is represented by red bars where colour intensity decreases with lower values of
percent identity between comparable blocks. Information on contigs such as the orientation, percent identity, coverage and overlap with
other contigs can also be visualized by loading the outputted feature file on ACT.
AUTHOR
ABACAS IS Copyright (C) 2008-10 The Wellcome Trust Sanger Institute, Cambridge, UK.
This manual page was written by Andreas Tille <tille@debian.org>, for the Debian project (and may be used by others).
1.3.1 2011-02-11 ABACAS(1)