Hi, all
I ever discussed the below questions with some members here, but not got clear answer yet. Anyone can help?
For pair-end reads, if the read1 is uniquely mapping, but its mate partner read2 is mapped in multiple places, how htseq deal with this situation? Count as one or throw this paired read?
After sorting my SAM file, it seems my SAM files is mixed with both single end and pair-end, to be clearer, the below is an example (only read name):
HWI-ST1106:1870NMUACXX:6:1101:10001:124778
HWI-ST1106:1870NMUACXX:6:1101:10001:124778
HWI-ST1106:1870NMUACXX:6:1101:10001:137376
HWI-ST1106:1870NMUACXX:6:1101:10001:138830
HWI-ST1106:1870NMUACXX:6:1101:10001:138830
My fastq file is properly paired. Looked my sam file, it seems that many one side read failed to align onto genom and thus only single end read is remained in SAM file.
Will the third uniquely mapped read "...137376" be counted by htseq? Before using Htseq, these scattered "single-end reads" should be filtered first?
To prevent producing this type of "single-end reads" in sam, from the tophat manual, it seems the parameter "--no-mixed" just do the work (only report alignments both pair reads mapped?). Is my understanding right?
thanks!
maize
I ever discussed the below questions with some members here, but not got clear answer yet. Anyone can help?
For pair-end reads, if the read1 is uniquely mapping, but its mate partner read2 is mapped in multiple places, how htseq deal with this situation? Count as one or throw this paired read?
After sorting my SAM file, it seems my SAM files is mixed with both single end and pair-end, to be clearer, the below is an example (only read name):
HWI-ST1106:1870NMUACXX:6:1101:10001:124778
HWI-ST1106:1870NMUACXX:6:1101:10001:124778
HWI-ST1106:1870NMUACXX:6:1101:10001:137376
HWI-ST1106:1870NMUACXX:6:1101:10001:138830
HWI-ST1106:1870NMUACXX:6:1101:10001:138830
My fastq file is properly paired. Looked my sam file, it seems that many one side read failed to align onto genom and thus only single end read is remained in SAM file.
Will the third uniquely mapped read "...137376" be counted by htseq? Before using Htseq, these scattered "single-end reads" should be filtered first?
To prevent producing this type of "single-end reads" in sam, from the tophat manual, it seems the parameter "--no-mixed" just do the work (only report alignments both pair reads mapped?). Is my understanding right?
thanks!
maize
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