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Old 12-01-2011, 07:47 AM   #21
asheenlevrai
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I'm not sure I got it right.

if there are more than 3 hits for a given read, then the XA tag will be removed and...
a) only 1 randomly chosen read will be reported (in the sam file)?
b) all hits will be reported, but as "independent" hits rather than as alternative hits?

thanx again
-a-
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Old 12-07-2011, 06:04 AM   #22
aggp11
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Quote:
Originally Posted by asheenlevrai View Post
I'm not sure I got it right.

if there are more than 3 hits for a given read, then the XA tag will be removed and...
a) only 1 randomly chosen read will be reported (in the sam file)?
b) all hits will be reported, but as "independent" hits rather than as alternative hits?

thanx again
-a-
What I meant was, (as far as I understand BWA's working) that for the default values, if BWA finds more than <=3 hits for a read, it still reports only 1 hit for that read (single line in the sam file), but it adds the XA tag to that read, with the other hits.

However, if there are more than 3 hits, BWA doesn't include the XA tag with the read information.

eg. Lets say after alignment, BWA found 2 hits for ABC:test:read (read name). 1st hit is at chr1:110228419 and the second hit is at chr10:96234821 In the SAM file, the row for this read would look something like this.

ABC:test:read 0 chr1 110228419 37 100M * ... XA:Z:chr10,96234821, 100M, 10;

However, if there are more than 3 hits for this read, the SAM file would look something like this:

ABC:test:read 0 chr1 110228419 37 100M * ...

BWA doesn't report alternative hits as separate rows. It just reports them in the XA tag for the read (if no. of hits <= -n INT).

Does this make more sense?
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Old 12-07-2011, 09:22 AM   #23
asheenlevrai
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Quote:
Originally Posted by aggp11 View Post
BWA doesn't report alternative hits as separate rows. It just reports them in the XA tag for the read (if no. of hits <= -n INT).

Does this make more sense?
Thank you. I didn't try to look at the SAM files "directly" actually. I just tried to open them in a graphical visualization program (which I am not familiar with, yet). I'll check that out...

I was wondering if the alternate reads (the ones on the same row with the 1st read, baring an XA tag) would be displayed in the visualization program. I guess it depends on the program...

Thank you very much for your help
-a-
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Old 12-08-2011, 07:25 AM   #24
asheenlevrai
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I used the galaxy website to process the data. I generated SAM files (alignments) from the different fastq files and then used SAM tools to convert SAM to BAM. Finally, I merged BAM files. There is no "merge SAM files" tools in SAM tools on the galaxy website. I bet there's a good reason for that... I'll check if there's a way to merge my SAM files, in order for me to compare the reads' XA tags and the output from the visualization program I will use (not determined which one yet, unsuccessful with most of them...).
-a-
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Old 12-08-2011, 10:04 AM   #25
asheenlevrai
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When I try to use IGV with a BAM file, it says
"Could not load index file for: /file_path
An index file is required for SAM & BAM files."
I don't know what this index file might be...
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Old 12-08-2011, 12:14 PM   #26
asheenlevrai
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Quote:
Originally Posted by aggp11 View Post
However, if there are more than 3 hits, BWA doesn't include the XA tag with the read information.

...

BWA doesn't report alternative hits as separate rows. It just reports them in the XA tag for the read (if no. of hits <= -n INT).

Does this make more sense?
I guess reads can be evaluated on their mapping quality, right?
if they have a positive mapping quality value, then they're unique reads...
if they have a mapping quality value of 0, then there are alternative hits...
if they have a mapping quality value of 0 and XA tag(s), then there are at most 3 alternative hits...
right?
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Old 01-13-2012, 01:29 PM   #27
asheenlevrai
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Something I don't understand:
In my BAM file, I have reads with a positive Mapping Quality (not =0) and XA tags... How is that even possible?
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Old 03-26-2012, 01:44 PM   #28
peas1127
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does anyone know the exact commands to simulate reads in stampy??

m doing
-S <filename>.fastQ -g hg -h hg

please tell me if thats correct??
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