9/17/2023 0 Comments View sam file linux![]() Not all mappers write the same information to a BAM file - most won't write unmapped reads unless you ask them to some will list reads that map to multiple sites in the genome multiple times, others only once, others never.Ī dirty secret is that these are often not published because they can raise questions that are uncomfortable or not easy to answer and often irrelevant to the subject of the publication. Not all mappers actually write data to that bitfield, or may not populate a field if you don't instruct the mapper right for example, if you have paired-end data but tell the mapper to map both reads as single-end reads, you won't get pairing stats. Therefore, idxstats gives the number of mapped read on each miRNA. In miRNA alignment, reference sequence name (3rd field in a sam file) is name of miRNA. For each sequence of the reference, it provides: Reports on stats related to the chromosome-based indexing done by samtools index.
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