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  #1  
Old 28th April 2014, 08:10 AM
felix felix is offline
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Posts: 816
Big-Y Telomere

I did a small experiment to see if I could extract the telomere length information from BigY BAM and indeed I was able to. So, I made a small tool using telseq on windows using cygwin so that anyone can use it.

Download: BigY Telomere (64 bit).zip (8.01 MB)
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  #2  
Old 28th April 2014, 08:28 AM
Ann Turner Ann Turner is offline
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If people post their results along with their age, it might be interesting to see if there's an inverse correlation. There's a lot of scatter in Figure 2 of the paper you cited.
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  #3  
Old 17th May 2014, 08:07 AM
wighty44 wighty44 is offline
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Join Date: Jan 2009
Location: Bridgeton, NJ
Posts: 142
Felix,
I just used this utility on my BAM file, but no telomere length was reported. The telomere.txt file only contained the line, "Telomere length:" - no values.

The BAM file processing messages are shown below:
[bigy.bam]
Start analyszing BAM bigy.bam
Specified BAM has 1 read group
[scan] processed 10000000 reads
[scan] total reads in BAM scanned 10533841
Completed scanning BAM
2 [main] telseq 2488 cygwin_exception: open_stackdumpfile: dumping stack trace to telseq.exe.stackdump
********** RESULT ************
/bin/cat: telseq.out: no such file or directory
Telomere Length:


I appended a txt extension to the attached telseq.exe.stackdump file to allow it to be uploaded here.
Attached Files
File Type: txt telseq.exe.stackdump.txt (1.9 KB, 3 views)
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  #4  
Old 17th May 2014, 08:10 AM
felix felix is offline
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Join Date: Mar 2013
Posts: 816
Quote:
Originally Posted by wighty44 View Post
Felix,
I just used this utility on my BAM file, but no telomere length was reported. The telomere.txt file only contained the line, "Telomere length:" - no values.

The BAM file processing messages are shown below:
[bigy.bam]
Start analyszing BAM bigy.bam
Specified BAM has 1 read group
[scan] processed 10000000 reads
[scan] total reads in BAM scanned 10533841
Completed scanning BAM
2 [main] telseq 2488 cygwin_exception: open_stackdumpfile: dumping stack trace to telseq.exe.stackdump
********** RESULT ************
/bin/cat: telseq.out: no such file or directory
Telomere Length:


I appended a txt extension to the attached telseq.exe.stackdump file to allow it to be uploaded here.
It depends on the BigY BAM. It seems some BigY BAM contains those details and some don't.
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  #5  
Old 17th May 2014, 08:22 AM
wighty44 wighty44 is offline
mtDNA H5b1 | Big Y Pending
 
Join Date: Jan 2009
Location: Bridgeton, NJ
Posts: 142
Quote:
Originally Posted by felix View Post
It depends on the BigY BAM. It seems some BigY BAM contains those details and some don't.
As luck would have it, it appears my BAM file did not contain the information.

It makes me wonder what factors are involved in that determination?
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  #6  
Old 17th May 2014, 08:25 AM
felix felix is offline
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Join Date: Mar 2013
Posts: 816
Quote:
Originally Posted by wighty44 View Post
As luck would have it, it appears my BAM file did not contain the information.

It makes me wonder what factors are involved in that determination?
I am not sure. I just included the telseq project as part of processing BAM.
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  #7  
Old 30th November 2014, 04:48 AM
PeterLarsen PeterLarsen is offline
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Join Date: Dec 2013
Posts: 185
Quote:
Originally Posted by wighty44 View Post
Felix,
I just used this utility on my BAM file, but no telomere length was reported. The telomere.txt file only contained the line, "Telomere length:" - no values.

The BAM file processing messages are shown below:
[bigy.bam]
Start analyszing BAM bigy.bam
Specified BAM has 1 read group
[scan] processed 10000000 reads
[scan] total reads in BAM scanned 10533841
Completed scanning BAM
2 [main] telseq 2488 cygwin_exception: open_stackdumpfile: dumping stack trace to telseq.exe.stackdump
********** RESULT ************
/bin/cat: telseq.out: no such file or directory
Telomere Length:


I appended a txt extension to the attached telseq.exe.stackdump file to allow it to be uploaded here.
I tried using the telseq-command today on my BigY BAM-file and got almost exactly the same result as you, also tried through cygwin.

Question is, is this something FTDNA is weeding out from the BAM-files in their quest to "protect" us? Or is it really random if this information gets through into the BAM?
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  #8  
Old 30th November 2014, 12:04 PM
RDickinson RDickinson is offline
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Join Date: Jul 2014
Posts: 68
Curious--just ran the BAM Analysis Kit and my telomere.txt file also lists no values--?
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  #9  
Old 30th November 2014, 01:49 PM
felix felix is offline
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Join Date: Mar 2013
Posts: 816
Based on what I read in several medical literature regarding telomeres, it is calculated mostly on WBC (white blood cells). What can be found in BigY BAM will not be accurate and it is only good to know fun stuff rather than any medical info in it.
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