Question: Samtools Flagstat Output
4
gravatar for Nitram
7.8 years ago by
Nitram60
Nitram60 wrote:

For past two hours I tried to browse around for samtools flagstat output information, unfortunately could not find much related to my problem - this is my samtool flagstat output for single end reads - does anyone think that the tophat alignment did not work well. Please let me know. Any possible replies would be greatly appreciated. Thanks in advance.

$ samtools flagstat accepted_hits.bam

18109074 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 18109074 + 0 mapped (100.00%:nan%) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (nan%:nan%) 0 + 0 with itself and mate mapped 0 + 0 singletons (nan%:nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)

samtools • 9.5k views
ADD COMMENTlink written 7.8 years ago by Nitram60
3
gravatar for Wen.Huang
7.8 years ago by
Wen.Huang1.2k
Wen.Huang1.2k wrote:

your output actually says all were mapped. I am pretty sure that top hat only outputs mapped reads. you need to compare the number to the input file.

ADD COMMENTlink written 7.8 years ago by Wen.Huang1.2k
1

It has to be multi-reads.

try

samtools view accepted_hits.bam | cut -f1 | sort | uniq | wc -l

this should give you the count of unique reads

ADD REPLYlink modified 6.6 years ago by Istvan Albert ♦♦ 81k • written 7.8 years ago by Wen.Huang1.2k
1

It has to be multi-reads. try "samtools view accepted_hits.bam | cut -f1 | sort | uniq | wc -l" this should give you the count of unique reads

ADD REPLYlink written 7.8 years ago by Wen.Huang1.2k

Thanks so much for your reply. My input fastq file has only 17,264,285 reads, then how could the number of mapped reads (~18,109,074) be higher.

ADD REPLYlink written 7.8 years ago by Nitram60

Is it possible that bowtie is outputting repetative reads multiple times? samtools flagstat would not try to account for this.

ADD REPLYlink written 7.8 years ago by Swbarnes21.5k

Thanks so much. It helped !

ADD REPLYlink written 7.7 years ago by Nitram60
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