2024 The index file is older than the fasta file

The index file is older than the fasta file

Author: fmqv

August undefined, 2024

WebAn index generated from the sequences with fasta-make-index which is named the same as the FASTA file but with ".index" appended. Sequence identifiers, either listed on the command line, from a file specified with -f option or provided on standard input. Output. Writes a FASTA format file to standard output. Options.

Error in string index out of range: maf file to fasta file

WebMay 25, 2024 · Yes, there are fasta sequences between the headers, and it has a large number of fasta sequences alongside their headers for each. I didn't know anything about Biopython, but I just looked it up and it seems really helpful as it has motif analysis tools (MEME or MAST). Thank you – taeju May 25, 2024 at 12:42 Add a comment 4 Answers … WebHow to solve problems with INDEX files. Associate the INDEX file extension with the correct application. On. Windows Mac Linux iPhone Android. , right-click on any INDEX file and … defra 2021 ghg conversion factors

What is the difference between FASTA, FASTQ, and SAM …

Web1. The headers in the input FASTA file must exactly match the chromosome column in the BED file. 2. You can use the UNIX fold command to set the line width of the FASTA output. … WebThe index file typically has the same filename as the corresponding FASTA/FASTQ file, with .fai appended. An fai index file is a text file consisting of lines each with five TAB … WebOct 22, 2024 · are you absolutely sure that fasta file and index files are in ~/correctpath/ and have the name that you're using? Are they all accessible in read mode? Which command … fen-bay hormann

getfasta — bedtools 2.30.0 documentation - Read the Docs

What is the difference between FASTA, FASTQ, and SAM file formats?

WebSep 20, 2024 · HDF5 files. HDF5 is a data model, library, and file format for storing and managing data. The SRA accepts bas.h5 and bax.h5 file submissions for PacBio-based submission and .fast5 files for submissions related to MinION Oxford Nanopore.. PacBio. Submission of data from the RS II instrument requires one (1) bas.h5 file and three (3) … WebJan 6, 2016 · -i : use when the ids in the id file are EXACTLY identical to those in the FASTA file -h : Show this help and exit. -o : will create one fasta file for each of the id files -s : will create one fasta file per id -n : means that the last arguments (after the sequence file) passed are a QUOTED list of the names desired. fenbar thornwood nyWebJul 5, 2024 · If the filename is empty it will be falsy, if not we can check index 0 because it's certainly will be there and index 0 of filename is index 2 of record. Second problem is to use the format string instead of + operator. It will convert anything you pass to the format string to a string as the format passed is %s. defra approved hypochlorous acid

"WebThe FASTA file itself may have been corrupted during download; delete the fasta file and the index and re-download (you can use the VEP installer to do this). Older versions of BioPerl … " - The index file is older than the fasta file

The index file is older than the fasta file

File Format Guide - National Center for Biotechnology Information

Web1 day ago · In it, more than 2.8 million people are described as having security clearance as of October 2024 – more than 1.6 million with access to either Confidential or Secret … Webkallisto index builds an index from a FASTA formatted file of target sequences. The arguments for the index command are: kallisto 0.46.0 Builds a kallisto index Usage: kallisto index [arguments] FASTA-files Required argument: -i, --index=STRING Filename for the kallisto index to be constructed Optional argument: -k, --kmer-size=INT k-mer (odd ...

Did you know?

WebJul 5, 2024 · If the filename is empty it will be falsy, if not we can check index 0 because it's certainly will be there and index 0 of filename is index 2 of record. Second problem is to … WebFASTQ files are named with the sample name and the sample number, which is a numeric assignment based on the order that the sample is listed in the sample sheet. ... the sequence observed in the index read is written to the FASTQ header in place of the sample number. This information can be useful for troubleshooting demultiplexing. ...

WebA bai file isn't an indexed form of a bam - it's a companion to your bam that contains the index.. A bam file is a binary blob that stores all of your aligned sequence data. You can view what's in the bam file using "samtools view bamfile.bam less".. Bam files can also have a companion file, called an index file. This file has the same name, suffixed with .bai. Web1 day ago · A 21-year-old member of the U.S. Air National Guard accused of leaking top secret military intelligence records online was charged on Friday with unlawfully copying …

WebFASTA and FASTQ formats are both file formats that contain sequencing reads while SAM files are these reads aligned to a reference sequence. In other words, FASTA and FASTQ … WebFeb 18, 2024 · Since some species of Pseudomonas have multiple sequences in the database (e.g., P. putida has 1.8k entries) I would like to know how many different species of Pseudomonas are there (in the 9k Pseudomonas entries), by names (i.e., in the filtered Psedumonas fasta file).

WebJan 16, 2011 · The FASTA index will be a file called volvox.fa.fai. Then we'll move these files into a "data directory" that JBrowse can use Then create the file data/tracks.conf with this file content [GENERAL] refSeqs=volvox.fa.fai [tracks.refseq] urlTemplate=volvox.fa storeClass=JBrowse/Store/SeqFeature/IndexedFasta type=Sequence

WebMar 26, 2024 · Please find attached file I want to find first index of arrays < 5 and then remove them from matrix (I want to filter arrays less than 5). I really appreciate any help. I deleted I got my answer, I attached again. Sign in to … fenbao chairsWebThe index files must have the same base file name and must reside in the same directory as the file that it indexes. For example, the index file for test-xyz.bam would be named test-xyz.bam.bai or test-xyz.bai. Multiple tools are available for sorting and indexing BAM files, including igvtools, the samtools package, and in GenePattern. defra background no2 mapsWebSep 25, 2024 · The index file produced by samtools faidx and .bai have very different structures. I guess there are mainly two reasons for it: In a bam file we have typically much more entrys than in a fasta file. The way we query the data. For a fasta file we typically ask "Give me the sequence with the id XY". defra codes of practiceWebThe compression of FASTA files requires a specific compressor to handle both channels of information: identifiers and sequence. For improved compression results, these are … fen bank greyhound sanctuaryhttp://www.htslib.org/doc/samtools-faidx.html fen axiooWebWrite a script to build the genome index file. We will use STAR to index the genome fasta file we just downloaded. We highly recommend you read and refer to the STAR manual when doing your own RNA-seq work, as it explains the meaning of all of the many parameters that are essential to produce an accurate, reliable STAR alignment.. For example, when … defra animal welfare actWebDESCRIPTION Index reference sequence in the FASTA format or extract subsequence from indexed reference sequence. If no region is specified, faidx will index the file and create … def racine python