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Search: Posts Made By: asheenlevrai
Forum: General 06-15-2012, 09:19 AM
Replies: 5
Views: 5,708
Posted By asheenlevrai
Apparently in Seaview you can't create a sequence...

Apparently in Seaview you can't create a sequence over 5kb... (it crops the sequence if you try to paste more than 5kb)
If you open a file (created with bioedit) containing sequences over 5kb,...
Forum: General 06-08-2012, 01:42 PM
Replies: 5
Views: 5,708
Posted By asheenlevrai
Well, yeah, we run BioEdit under WINE on mac but...

Well, yeah, we run BioEdit under WINE on mac but there are limitations... We can't print or access our NAS for instance... We can't open sequence files directly neither: we have to launch BioEdit and...
Forum: General 06-08-2012, 09:51 AM
Replies: 5
Views: 5,708
Posted By asheenlevrai
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...
Forum: General 04-11-2012, 12:29 PM
Replies: 5
Views: 5,708
Posted By asheenlevrai
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...
Forum: General 01-18-2012, 06:30 AM
Replies: 3
Views: 4,204
Posted By asheenlevrai
I was using BWA via the galaxy project website

I was using BWA via the galaxy project website
Forum: General 01-17-2012, 12:08 PM
Replies: 3
Views: 4,204
Posted By asheenlevrai
Anyone has an idea how reads with XA tags can...

Anyone has an idea how reads with XA tags can have a mapping quality >0?

These reads also have XT = U, meaning they should be unique, right? how can reads have XT=U and multiple XA tags???
Forum: General 01-15-2012, 03:32 PM
Replies: 3
Views: 4,204
Posted By asheenlevrai
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).
...
Forum: General 01-13-2012, 01:29 PM
Replies: 27
Views: 9,439
Posted By asheenlevrai
Something I don't understand: In my BAM file, I...

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?
Forum: General 01-04-2012, 08:01 AM
Replies: 7
Views: 4,518
Posted By asheenlevrai
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...
Forum: General 12-31-2011, 03:37 PM
Replies: 4
Views: 2,087
Posted By asheenlevrai
mRNA 5' end reads

mRNA 5' end reads
Forum: General 12-30-2011, 12:06 PM
Replies: 7
Views: 4,518
Posted By asheenlevrai
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...
Forum: General 12-29-2011, 10:43 AM
Replies: 4
Views: 2,087
Posted By asheenlevrai
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 =...
Forum: General 12-29-2011, 10:35 AM
Replies: 0
Views: 1,261
Posted By asheenlevrai
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...
Forum: General 12-29-2011, 10:18 AM
Replies: 7
Views: 4,518
Posted By asheenlevrai
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...
Forum: General 12-08-2011, 12:14 PM
Replies: 27
Views: 9,439
Posted By asheenlevrai
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...
Forum: General 12-08-2011, 10:04 AM
Replies: 27
Views: 9,439
Posted By asheenlevrai
When I try to use IGV with a BAM file, it says ...

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...
Forum: General 12-08-2011, 07:25 AM
Replies: 27
Views: 9,439
Posted By asheenlevrai
I used the galaxy website to process the data. I...

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...
Forum: General 12-07-2011, 09:22 AM
Replies: 27
Views: 9,439
Posted By asheenlevrai
Thank you. I didn't try to look at the SAM files...

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...
Forum: General 12-01-2011, 07:47 AM
Replies: 27
Views: 9,439
Posted By asheenlevrai
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...
Forum: General 11-30-2011, 08:28 AM
Replies: 27
Views: 9,439
Posted By asheenlevrai
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
...
Forum: General 11-08-2011, 08:06 AM
Replies: 27
Views: 9,439
Posted By asheenlevrai
Well since I get the same quality values when I...

Well since I get the same quality values when I download the .fastq files from NCBI or when I use fastq-dump on the .sar file, why wouldn't I just use the downloadable .fastq files? The reads are...
Forum: General 11-07-2011, 12:29 PM
Replies: 27
Views: 9,439
Posted By asheenlevrai
So I used the "fastq-dump" command from the "SRA...

So I used the "fastq-dump" command from the "SRA toolkit" in order to convert 1 of the .sra files to .fastq
I compared (using textedit) this file to the correponding .fastq file I downloaded from...
Forum: General 11-07-2011, 11:05 AM
Replies: 27
Views: 9,439
Posted By asheenlevrai
So it would be more like: 1) convert .sar files...

So it would be more like:
1) convert .sar files to .fastq files using dump-fastq.
I don't know how to do that. Should I install the "SRA toolkit"?

2) align .fastq files to the mouse genome to...
Forum: General 11-07-2011, 10:47 AM
Replies: 27
Views: 9,439
Posted By asheenlevrai
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...
Forum: General 11-07-2011, 10:27 AM
Replies: 27
Views: 9,439
Posted By asheenlevrai
do you mean I could align the (millions of) reads...

do you mean I could align the (millions of) reads contained in 20 .fastq files to the mouse genome? I mean, without getting 20 alignment files at the end, but a single one to look at with a viewer......
Showing results 1 to 25 of 28

 


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