Forum: General
06-15-2012, 09:19 AM
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Replies: 5
Views: 5,851
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Forum: General
06-08-2012, 01:42 PM
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Replies: 5
Views: 5,851
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Forum: General
06-08-2012, 09:51 AM
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Replies: 5
Views: 5,851
Thank you :)
I didn't try Geneious nor...
Thank you :)
I didn't try Geneious nor Vector NTI since they are not free... (oh and because I hate Vector NTI...)
I didn't try Consed because of the reasons you mentioned ;)
As far as I...
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Forum: General
04-11-2012, 12:29 PM
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Replies: 5
Views: 5,851
BioEdit file viewer for mac
Hi everyone,
Does anyone knows how to view (and print) BioEdit alignment files on a mac?
I would be very happy if anything exists with the option to display same bases as a dot (it makes it much...
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Forum: General
01-18-2012, 06:30 AM
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Replies: 3
Views: 4,329
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Forum: General
01-17-2012, 12:08 PM
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Replies: 3
Views: 4,329
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Forum: General
01-15-2012, 03:32 PM
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Replies: 3
Views: 4,329
IGV: Mapping Quality vs. XA tag (I'm lost)
Hello all,
In IGV, reads with a mapping quality = 0 are displayed in white while reads
with a positive mapping quality are displayed in grey (at least for the bam
file I am trying to analyze).
...
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Forum: General
01-13-2012, 01:29 PM
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Replies: 27
Views: 9,699
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Forum: General
01-04-2012, 08:01 AM
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Replies: 7
Views: 4,849
I'm happy I could help.
I'm sorry but I am not...
I'm happy I could help.
I'm sorry but I am not so familiar with clustal and I don't want to give you inaccurate info. However you will probably easily get a confirmation online or in some clustal...
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Forum: General
12-31-2011, 03:37 PM
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Replies: 4
Views: 2,176
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Forum: General
12-30-2011, 12:06 PM
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Replies: 7
Views: 4,849
well, I think I see what you're doing.
You try...
well, I think I see what you're doing.
You try to open your sequence files as if they were bioedit (alignment) files, using file->open or something, right?
In my hands, this does not work very...
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Forum: General
12-29-2011, 10:43 AM
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Replies: 4
Views: 2,176
how to get rid of adapter sequences
Hello,
I received a dataset of reads that are supposed to have the following format:
bases (1-3) = 3bp fingerprint (I know what this sequence should be)
bases 4-28 = 25bp read
bases 29-36 =...
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Forum: General
12-29-2011, 10:35 AM
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Replies: 0
Views: 1,309
BWA, I don't know what I'm doing
Hello,
I'm not really sure I understand how to setup parameters in BWA.
I want to map 25bp non-paired reads to the mouse genome. I try to do that on galaxy...
I made an alignment using the...
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Forum: General
12-29-2011, 10:18 AM
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Replies: 7
Views: 4,849
Hi,
I use bioedit (which is not maintained...
Hi,
I use bioedit (which is not maintained anymore), but only to compare short sequences (a few kb max). I usually align them manually but you can also use the clustalW plugin that is provided in...
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Forum: General
12-08-2011, 12:14 PM
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Replies: 27
Views: 9,699
I guess reads can be evaluated on their mapping...
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...
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Forum: General
12-08-2011, 10:04 AM
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Replies: 27
Views: 9,699
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Forum: General
12-08-2011, 07:25 AM
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Replies: 27
Views: 9,699
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Forum: General
12-07-2011, 09:22 AM
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Replies: 27
Views: 9,699
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Forum: General
12-01-2011, 07:47 AM
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Replies: 27
Views: 9,699
I'm not sure I got it right.
if there are...
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...
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Forum: General
11-30-2011, 08:28 AM
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Replies: 27
Views: 9,699
Hello again,
Can someone explain me, in...
Hello again,
Can someone explain me, in simple words, what the samse -n option does in BWA?
the man says :
"-n INT Maximum number of alignments to output in the XA tag for reads paired
...
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Forum: General
11-08-2011, 08:06 AM
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Replies: 27
Views: 9,699
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Forum: General
11-07-2011, 12:29 PM
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Replies: 27
Views: 9,699
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Forum: General
11-07-2011, 11:05 AM
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Replies: 27
Views: 9,699
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Forum: General
11-07-2011, 10:47 AM
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Replies: 27
Views: 9,699
Is that due to
"note that the NCBI have...
Is that due to
"note that the NCBI have converted this FASTQ data from the original Solexa/Illumina encoding to the Sanger standard"
?
by "cooking" you mean going back to the illumina...
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Forum: General
11-07-2011, 10:27 AM
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Replies: 27
Views: 9,699
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