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Hello everyone,
I use the data from the sra website.
for executing Tophat I use the command:
Tophat gives no warnings:
The output of samtools flagstat on accepted_hits.bam:
The output of unmapped.bam:
What did I do wrong, because this is a very low mapping percentage...
I use the data from the sra website.
for executing Tophat I use the command:
Code:
tophat2 -a 5 -m 2 -N 10 -x 1 --read-edit-dist 12 -o <outDir> <reference genome> SRR493747.fastq
Code:
2013-05-16 13:52:13] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-05-16 13:52:13] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version: 0.12.7.0
[2013-05-16 13:52:13] Checking for Samtools
Samtools version: 0.1.8.0
[2013-05-16 13:52:13] Checking for Bowtie index files
[2013-05-16 13:52:13] Checking for reference FASTA file
[2013-05-16 13:52:13] Generating SAM header for /home/fedor/GENOMES/H_sapiens/H_sapiens_GRCh37
format: fastq
quality scale: phred33 (default)
[2013-05-16 13:52:33] Preparing reads
left reads: min. length=50, max. length=50, 999961 kept reads (39 discarded)
[2013-05-16 13:52:46] Mapping left_kept_reads to genome H_sapiens_GRCh37 with Bowtie
[2013-05-16 14:03:40] Mapping left_kept_reads_seg1 to genome H_sapiens_GRCh37 with Bowtie (1/2)
[2013-05-16 14:13:51] Mapping left_kept_reads_seg2 to genome H_sapiens_GRCh37 with Bowtie (2/2)
[2013-05-16 14:22:17] Searching for junctions via segment mapping
[2013-05-16 14:25:39] Retrieving sequences for splices
[2013-05-16 14:28:49] Indexing splices
[2013-05-16 14:28:49] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie (1/2)
[2013-05-16 14:29:10] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie (2/2)
[2013-05-16 14:29:33] Joining segment hits
[2013-05-16 14:31:39] Reporting output tracks
-----------------------------------------------
[2013-05-16 14:33:46] Run complete: 00:41:32 elapsed
Code:
5 in total 0 QC failure 0 duplicates 25 mapped (100.00%) 0 paired in sequencing 0 read1 0 read2 0 properly paired (nan%) 0 with itself and mate mapped 0 singletons (nan%) 0 with mate mapped to a different chr 0 with mate mapped to a different chr (mapQ>=5)
Code:
999993 in total 39 QC failure 0 duplicates 0 mapped (0.00%) 0 paired in sequencing 0 read1 0 read2 0 properly paired (nan%) 0 with itself and mate mapped 0 singletons (nan%) 0 with mate mapped to a different chr 0 with mate mapped to a different chr (mapQ>=5)