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What is the difference between BAM and FASTQ?
BAM files are also much more compact than compressed FASTQ or FASTA files. FASTA to store the reference genome/transcriptome that the sequence fragments will be mapped to. FASTQ to store the sequence fragments before mapping. SAM/BAM to store the sequence fragments after mapping.
What does FASTQ file stand for?
A FASTQ file is a text file that contains the sequence data from the clusters that pass filter on a flow cell (for more information on clusters passing filter, see the “additional information” section of this bulletin). If samples were multiplexed, the first step in FASTQ file generation is demultiplexing.
How to create two FASTQ files in Bam?
If your BAM alignments are from paired-end sequence data, one can use the -fq2 option to create two distinct FASTQ output files — one for end 1 and one for end 2. When using this option, it is required that the BAM file is sorted/grouped by the read name. This keeps the resulting records in the two output FASTQ files in the same order.
When to use BAM for paired FASTQ in BedTools?
Used if BAM contains paired-end data. BAM should be sorted by query name ( samtools sort -n -o aln.qsort.bam aln.bam) if creating paired FASTQ with this option. Create FASTQ based on the mate info in the BAM R2 and Q2 tags. By default, each alignment in the BAM file is converted to a FASTQ record in the -fq file.
How to sort BAM file by read name?
When using this option, it is required that the BAM file is sorted/grouped by the read name. This keeps the resulting records in the two output FASTQ files in the same order. One can sort the BAM file by query name with samtools sort -n -o aln.qsort.bam aln.bam.
How to redetect Bam to fastqsanger datatype?
But you can use the Edit-Attributes > Datatypes > Redetect datatype function to get this reassigned to the fastqsanger datatype. Then downstream tools will recognize it. If the input is paired-end mapped BAM, in the default format (coordinate sorted), the tool will behave oddly.