The index file is older than the fasta file

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August undefined, 2024

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

WebJan 15, 2024 · [W::hts_idx_load2] The index file is older than the data file: /path_to/ALL.chr6_GRCh38.genotypes.20240504.vcf.gz.tbi There was no error in the … WebThe compression of FASTA files requires a specific compressor to handle both channels of information: identifiers and sequence. For improved compression results, these are … six flags tickets atlanta discount

should FASTA files be sorted before indexed with SAMtools?

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 … WebSep 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". WebJun 2, 2024 · I have a fasta file and I want to replace the seq Ids (description lines) with new and extended IDs. This is the format of fasta file: >3C-assembly contig_74 ... ($0, 2)) and using this value as array index. If the id is not empty, print > and the id and skip to the next record. The 1 prints the current record (the sequences or non-matching ids ... six flags tickets buy in advance discount

FASTX — pyfastx 1.0.1 documentation - Read the Docs

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WebJul 2, 2024 · [W::hts_idx_load2] The index file is older than the data file:PATH_TO_FILE/BH10281_1.bai. The files BH10281_1.bai and BH10281_1.bam as per 'Date Created' column were made at the same time. What exactly is this warning referring … WebWrite 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 … six flags tickets at the gateWebThe 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. six flags tickets cheaper online

"WebDESCRIPTION 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 … " - The index file is older than the fasta file

The index file is older than the fasta file

How can I find index of nearest value to specific number

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. 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 …

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WebJan 30, 2013 · fastahack is a small application for indexing and extracting sequences and. subsequences from FASTA files. The included Fasta.cpp library provides a FASTA. reader and indexer that can be embedded into applications which would benefit. from directly reading subsequences from FASTA files. The library automatically. WebApr 10, 2024 · Yes, officials say — at least, for the most part. U.S. officials are alarmed at the exposure of secret information, and the Federal Bureau of Investigation is working to …

WebMake an index for a FASTA file for use by fasta-fetch. Input The name of a file of sequences in FASTA format. Output. Writes an index file to .index. Options. Option Parameter Description Default Behavior; General Options-f : Overwrite an existing file if one exists. WebDESCRIPTION Using an fai index file in conjunction with a FASTA/FASTQ file containing reference sequences enables efficient access to arbitrary regions within those reference sequences. The index file typically has the same filename as the corresponding FASTA/FASTQ file, with .fai appended.

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) … 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 …

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 …

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. … six flags tickets coupons cokeWeb1 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 information and nearly 1.2 ... six flags tickets caWebFeb 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). six flags tickets grocery storehttp://www.htslib.org/doc/samtools-faidx.html six flags tickets low priceWebThe index file can be reused to save time when you read sequences from FASTA file next time. FASTA records iteration ¶ The fastest way to iterate plain or gzipped FASTA file without building index, the iteration will return a tuple contains name and sequence. six flags tickets discount walmartWebUsing an fai index file in conjunction with a FASTA file containing reference sequences enables efficient access to arbitrary regions within those reference sequences. The index file typically has the same filename as the corresponding FASTA file, with .fai appended. An fai index file is a text file consisting of lines each with five TAB ... six flags tickets costWebDec 17, 2004 · The index file may have additional structure, e.g., be a B-tree. See also inverted index, forward index. Note: An index file is helpful if records are large: the keys … six flags tickets discount code