52.68% = (2*(4647893+779552+138165) + 510907 + 357302)/(2*11389273)
Samtools is correct, since if sum the numerator you'll get just under 12 million total alignments, which is exactly what's in the BAM file (14328481-2329052).
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
hisat2 output more reads than are in the file
Hi all,
I am in the middle of testing the hisat2 mapper and encountered a discrepancy between the output hisat2 gives me at the end of the mapping step and the number of reads samtools flagstat counts.
this is the output I get, when hisat2 is finished:
Code:cat ../hisat2Mapping/WCE7.stat [B]11389273[/B] reads; of these: 11389273 (100.00%) were paired; of these: 5961828 (52.35%) aligned concordantly 0 times 4647893 (40.81%) aligned concordantly exactly 1 time 779552 (6.84%) aligned concordantly >1 times ---- 5961828 pairs aligned concordantly 0 times; of these: 138165 (2.32%) aligned discordantly 1 time ---- 5823663 pairs aligned 0 times concordantly or discordantly; of these: 11647326 mates make up the pairs; of these: 10779117 (92.55%) aligned 0 times 510907 (4.39%) aligned exactly 1 time 357302 (3.07%) aligned >1 times 52.68% overall alignment rate
and this is the number of reads I get, when I run samtools flagstat on the sorted/indexed bam file:
Code:samtools flagstat ../hisat2Mapping/WCE7.sorted.bam [B]14328481[/B] + 0 in total (QC-passed reads + QC-failed reads) 2329052 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 14328481 + 0 mapped (100.00%:-nan%) 11999429 + 0 paired in sequencing 6098403 + 0 read1 5901026 + 0 read2 10854890 + 0 properly paired (90.46%:-nan%) 11407498 + 0 with itself and mate mapped 591931 + 0 singletons (4.93%:-nan%) 23248 + 0 with mate mapped to a different chr 18678 + 0 with mate mapped to a different chr (mapQ>=5)
Is there a simple explanation for that?
thanks,
Assa
Latest Articles
Collapse
-
by seqadmin
The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
Channel: Articles
07-08-2024, 03:19 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 07-25-2024, 06:46 AM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
07-25-2024, 06:46 AM
|
||
Started by seqadmin, 07-24-2024, 11:09 AM
|
0 responses
28 views
0 likes
|
Last Post
by seqadmin
07-24-2024, 11:09 AM
|
||
Started by seqadmin, 07-19-2024, 07:20 AM
|
0 responses
161 views
0 likes
|
Last Post
by seqadmin
07-19-2024, 07:20 AM
|
||
Started by seqadmin, 07-16-2024, 05:49 AM
|
0 responses
127 views
0 likes
|
Last Post
by seqadmin
07-16-2024, 05:49 AM
|
Leave a comment: