Dear Friends,
When I run tophat to align RNA-Seq reads, the log file shows that some reads are discarded as below. Does anyone know why they are discarded? low quality reads? How can I setup the threshold for reads discarding?
Thank you very much.
[2015-01-25 22:24:21] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2015-01-25 22:24:21] Checking for Bowtie
Bowtie version: 2.1.0.0
[2015-01-25 22:24:21] Checking for Samtools
Samtools version: 0.1.19.0
[2015-01-25 22:24:21] Checking for Bowtie index files
[2015-01-25 22:24:21] Checking for reference FASTA file
[2015-01-25 22:24:21] Generating SAM header for musculus
format: fastq
quality scale: phred33 (default)
[2015-01-25 22:24:44] Reading known junctions from GTF file
[2015-01-25 22:24:48] Preparing reads
left reads: min. length=101, max. length=101, 6682858 kept reads (653 discarded)
right reads: min. length=101, max. length=101, 6641398 kept reads (42113 discarded)
When I run tophat to align RNA-Seq reads, the log file shows that some reads are discarded as below. Does anyone know why they are discarded? low quality reads? How can I setup the threshold for reads discarding?
Thank you very much.
[2015-01-25 22:24:21] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2015-01-25 22:24:21] Checking for Bowtie
Bowtie version: 2.1.0.0
[2015-01-25 22:24:21] Checking for Samtools
Samtools version: 0.1.19.0
[2015-01-25 22:24:21] Checking for Bowtie index files
[2015-01-25 22:24:21] Checking for reference FASTA file
[2015-01-25 22:24:21] Generating SAM header for musculus
format: fastq
quality scale: phred33 (default)
[2015-01-25 22:24:44] Reading known junctions from GTF file
[2015-01-25 22:24:48] Preparing reads
left reads: min. length=101, max. length=101, 6682858 kept reads (653 discarded)
right reads: min. length=101, max. length=101, 6641398 kept reads (42113 discarded)
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