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Samtools Extract Mapped Reads
Samtools Extract Mapped Reads. N/a) 58201619 + 0 paired in sequencing 29103737 + 0 read1 29097882 + 0 read2 0 + 0 properly paired (0.00% : The command in your second set:

Rsem is licensed under the gnu general public license v3. Count reads mapped to references from a bam stream. See the sam file format specification for details about the sam alignment format.
This Option Directs Stringtie To Operate In Expression.
N/a) 58201619 + 0 primary mapped (100.00% : Count reads mapped to references from a bam stream. Supplementary table 1) using bwa 35 and converted to the bam file format with samtools 36.
See The Sam File Format Specification For Details About The Sam Alignment Format.
Rsem is licensed under the gnu general public license v3. From my understanding your first command extracts all mapped reads, but does not extract mates that were unmapped. N/a) 58201619 + 0 paired in sequencing 29103737 + 0 read1 29097882 + 0 read2 0 + 0 properly paired (0.00% :
Subsequently, We Used Samtools V.1.3 (Ref.
The command in your second set: Prints help message and exits.
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