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Illumina MiSeqFGx - fastq vs. StrResults.txt
Hey,
I'll write my Bachelor Thesis in a few weeks and I'm new to NGS, so maybe this is quite a noob question -
however, these ar my problems:
1)
We are sequencing different markers like D3S1358, D22S1045 and so on with our new Illumina MiSeqFGx. Now I opened the Alignment/Report/StrResults.txt and found a result like the following for one sample:
Marker Allele Depth Sequence
D22S1045 16 23 ATTATTATTATTATTATTATTATTATTATTATTATTATTACTATTATT
D22S1045 17 78 ATTATTATTATTATTATTATTATTATTATTATTATTATTATTACTATTATT
OK, so this sample has Alleles 16,17 for D22S1045 marker.
Now I thought that all of the primer matching Sequences are stored in the .fastq files, so I started searching for the sequences in the .fastq files but havent found them.
(grep -c ATTATTATTATTATTATTATTATTATTATTATTATTATTATTACTATTATT Sample.fastq/data --> Result = 0)
What am I misunderstanding, I thought the reported sequences must be found in the .fastq file? Can anybody help?
2)
We determined the alleles with capillary electrophoresis before and now with NGS we have some other alleles as result for some samples. Sometimes Alleles determined with capillary electrophoresis arent even found by NGS and sometimes NGS finds more alleles for the same marker and the same sample than capillary electrophoresis. The StrResults.txt for example shows up 4 possible alleles and takes those with the highest depth value which is OK but someimes it only takes the one allele with the highest depth value ignoring the ones with slightly lower depth... I just dont get it...
Sorry for my bad english
I'll write my Bachelor Thesis in a few weeks and I'm new to NGS, so maybe this is quite a noob question -
however, these ar my problems:1)
We are sequencing different markers like D3S1358, D22S1045 and so on with our new Illumina MiSeqFGx. Now I opened the Alignment/Report/StrResults.txt and found a result like the following for one sample:
Marker Allele Depth Sequence
D22S1045 16 23 ATTATTATTATTATTATTATTATTATTATTATTATTATTACTATTATT
D22S1045 17 78 ATTATTATTATTATTATTATTATTATTATTATTATTATTATTACTATTATT
OK, so this sample has Alleles 16,17 for D22S1045 marker.
Now I thought that all of the primer matching Sequences are stored in the .fastq files, so I started searching for the sequences in the .fastq files but havent found them.
(grep -c ATTATTATTATTATTATTATTATTATTATTATTATTATTATTACTATTATT Sample.fastq/data --> Result = 0)
What am I misunderstanding, I thought the reported sequences must be found in the .fastq file? Can anybody help?
2)
We determined the alleles with capillary electrophoresis before and now with NGS we have some other alleles as result for some samples. Sometimes Alleles determined with capillary electrophoresis arent even found by NGS and sometimes NGS finds more alleles for the same marker and the same sample than capillary electrophoresis. The StrResults.txt for example shows up 4 possible alleles and takes those with the highest depth value which is OK but someimes it only takes the one allele with the highest depth value ignoring the ones with slightly lower depth... I just dont get it...
Sorry for my bad english
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