Hello all.
I am doing analysis of Illumina GAII/GAIIx data. I am working with female samples.
When I map the data, I see hits on chromosome Y.
The hits match perfectly and uniquely. Some of the reads were 36 bases, others were 100 bases.
To double-check the alignment, I used BLAT of the full sequence against hg18 (in the UCSC browser)
I also ran BLAT against hg16, hg17, hg19
I also did a BLAST search against hg18 (UCSC version) and NCBI Build 36.
No matter what I ran, I got hits to chromosome Y.
Specifics:
1. This has happened on 3 different samples (tumor cell line, blood sample, hESC female) prepped at different times
2. This has happened in two different laboratories. One has a GAII and the other has a GAIIx.
3. The samples were prepared and sequenced by different people. Two of the samples were prepared by females and sequenced by a female. The third sample was prepared by a female and sequenced by a male.
4. One sample was chip-seq, one was paired end genomic, one was paired-end exome (captured with NimbleGen's SeqCap)
5. All three samples were mapped with ELAND. One of the samples was also mapped with MAQ
Sooo....
#1 rules out contamination in the sample
#2 rules out contamination in the lab, on the cluster station and on the GA
#3 rules out contamination by a person
#4 rules out an artifact of the type of sequencing
#5 rules out an artifact of the type of mapping
We know the samples are female with no Y chromosome.
Has anyone run into this? Does anyone have any thoughts?
Thanks,
Lee
I am doing analysis of Illumina GAII/GAIIx data. I am working with female samples.
When I map the data, I see hits on chromosome Y.
The hits match perfectly and uniquely. Some of the reads were 36 bases, others were 100 bases.
To double-check the alignment, I used BLAT of the full sequence against hg18 (in the UCSC browser)
I also ran BLAT against hg16, hg17, hg19
I also did a BLAST search against hg18 (UCSC version) and NCBI Build 36.
No matter what I ran, I got hits to chromosome Y.
Specifics:
1. This has happened on 3 different samples (tumor cell line, blood sample, hESC female) prepped at different times
2. This has happened in two different laboratories. One has a GAII and the other has a GAIIx.
3. The samples were prepared and sequenced by different people. Two of the samples were prepared by females and sequenced by a female. The third sample was prepared by a female and sequenced by a male.
4. One sample was chip-seq, one was paired end genomic, one was paired-end exome (captured with NimbleGen's SeqCap)
5. All three samples were mapped with ELAND. One of the samples was also mapped with MAQ
Sooo....
#1 rules out contamination in the sample
#2 rules out contamination in the lab, on the cluster station and on the GA
#3 rules out contamination by a person
#4 rules out an artifact of the type of sequencing
#5 rules out an artifact of the type of mapping
We know the samples are female with no Y chromosome.
Has anyone run into this? Does anyone have any thoughts?
Thanks,
Lee
Comment