Cannot use index file with textual sam file
WebIf the index is not named in the standard manner, not located in the same directory as the BAM/CRAM file, or is remote. Without an index, random access via fetch () and pileup () is disabled. For writing, the header of a SAM file/ BAM file can be constituted from several sources (see also the samtools format specification): WebTablet will attempt to load a text-based .sam file, with or without SAM headers. A SAM file does not include reference/consensus information, so if it is to be included, it must be provided in a separate fasta/fastq file. When processing the CIGAR information from a SAM file, Tablet will create a list of features (that will be shown in the ...
Cannot use index file with textual sam file
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WebIndex a coordinate-sorted BAM or CRAM file for fast random access. (Note that this does not work with SAM files even if they are bgzip compressed — to index such files, use tabix (1) instead.) This index is needed when region arguments are used to limit samtools view and similar commands to particular regions of interest. WebConsider using samtools collate instead if you need name collated data without a full lexicographical sort. Note that if the sorted output file is to be indexed with samtools index , the default coordinate sort must be used. Thus the -n and -t options are incompatible with samtools index . OPTIONS -K INT
WebDec 1, 2015 · And now create the SAM file. bowtie2 -f -p 4 -x outputfilename -U input_reads.fna > input.output.sam. -f means the input is fasta (use -q for fastaq) -p is the number of processors to use: increase this on rambox! -x is the bowtie index file from bowtie2-build. -U is the file to search. Now we have a sam file, we need to convert that … WebOct 21, 2024 · samtools index -c SRR3438555.sorted.bam [E::hts_idx_push] Region 536881483..536881484 cannot be stored in a csi index with min_shift = 14, n_lvls = 5. …
WebAh, okay, so you definitely don't have a bam file, as u/brrrlinguist suggested -if you're able to edit it with sed it's a text file of some sort, not binary. My guess is that it was a SAM file … Webtabix file A sorted, compressed and indexed tab-separated file created by the command line tool tabix or the commands tabix_compress () and tabix_index (). The file is indexed by chromosomal coordinates. tabix row A row in a tabix file. Fields within a row are tab-separated. TAM Text SAM file.
WebInclude customized index file as a part of arguments. See EXAMPLES section for sample of usage. Output Options:-o, --output FILE. Write pileup output to FILE, rather than the default of standard output.-O, --output-BP. Output base positions on reads in orientation listed in the SAM file (left to right).--output-BP-5
WebIt says that the index file that I generated from samtools is not recognized. When I use the sorted file (from samtools too) and the IGV tries to generate an index file, it now says … take measures to do somethingWebCreate a file with the sample SAM content from above and adjust the path "example.sam" to the path to your SAM file (e.g. "/path/to/my_example.sam" ). Solution more... Accessing the Header ¶ Sequence information (i.e. @SQ records) from the BAM header is stored in the BamIOContext . take measures to do还是doingWebMAF Mutation Files; VCF Variant Files; Multi-Locus View; Regions of Interest; Sample Attributes; Sorting, Grouping, and Filtering; Saving and Restoring Sessions; Server … twist of fate indian series