The index file is older than the fasta file

Author: pzlh

August undefined, 2024

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). 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.

How can I find index of nearest value to specific number

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. … 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". isha supplements

getfasta — bedtools 2.30.0 documentation - Read the Docs

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 … 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 ... 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 information and nearly 1.2 ... safari thailande

FastQ Files - BaseSpace Sequence Hub - Illumina, Inc.

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 … http://www.htslib.org/doc/samtools-faidx.html isha systemWeb1 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 and transmitting classified ... safari theater sets

"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 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. " - The index file is older than the fasta file

The index file is older than the fasta file

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 … WebThe 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.

Did you know?

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 … 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.

WebTo do this, the program creates an index file that contains one entry for each sequence. If the FASTA file is named path/sequence.fasta, the index file is usually named path/sequence.fasta.fai. Using such index files, it is possible to rapidly read parts of the given sequence 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 …

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) … WebNov 29, 2024 · Index files on Windows 10. To index files for faster search results, you’ll need to make a search. Hit the Window key on your keyboard and type “indexing” and you’re …

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.

isha surgicalWebThe compression of FASTA files requires a specific compressor to handle both channels of information: identifiers and sequence. For improved compression results, these are … safari thatch davie flWebJun 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 ... isha summer campWebThe 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 … isha summerWeb1 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 … safari thatch and bambooWebDESCRIPTION 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 … safari theatre moorheadWebThe 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. safari theater mn