SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 75
Search took 0.01 seconds.
Search: Posts Made By: Jim Robinson
Forum: Bioinformatics 11-01-2015, 01:56 PM
Replies: 16
Views: 3,868
Posted By Jim Robinson
The reads look more or less evenly distributed...

The reads look more or less evenly distributed between strands, when colored by first-in-pair strand. Also, the junctions look more or less even between strands. It just has the look of an...
Forum: Bioinformatics 11-01-2015, 07:04 AM
Replies: 16
Views: 3,868
Posted By Jim Robinson
I ask because it doesn't appear to be strand...

I ask because it doesn't appear to be strand preserving. I would verify that with the lab you received it from.
Forum: Bioinformatics 11-01-2015, 12:48 AM
Replies: 16
Views: 3,868
Posted By Jim Robinson
No, I mean the library prep for the RNA, e.g....

No, I mean the library prep for the RNA, e.g. dUTP.
Forum: Bioinformatics 11-01-2015, 12:14 AM
Replies: 16
Views: 3,868
Posted By Jim Robinson
Hi, what protocol was used to prepare the...

Hi, what protocol was used to prepare the library?
Forum: General 06-17-2013, 06:04 AM
Replies: 4
Views: 7,590
Posted By Jim Robinson
Hi, This is not something IGV currently...

Hi,

This is not something IGV currently does. As you can see from my last post I'm not clear on the specifics of how a consensus sequence is defined, other than as a pileup. Some decision needs...
Forum: Bioinformatics 02-03-2013, 03:33 AM
Replies: 8
Views: 3,272
Posted By Jim Robinson
You can optionally display the soft-clipped...

You can optionally display the soft-clipped reads, its a user preference (View > Preferences > Alignments tab).
Forum: Bioinformatics 01-16-2013, 05:20 AM
Replies: 11
Views: 14,472
Posted By Jim Robinson
Why don't you just load the blat output (.psl...

Why don't you just load the blat output (.psl file)?
Forum: Bioinformatics 12-12-2012, 07:41 AM
Replies: 4
Views: 1,972
Posted By Jim Robinson
I'm a bit puzzled because the aliasing should not...

I'm a bit puzzled because the aliasing should not be necessary in this case. This is done automatically for sequences that start with "gi|". So gi|123456789|ref|NW_123456789.1| should...
Forum: Bioinformatics 12-12-2012, 05:54 AM
Replies: 4
Views: 1,972
Posted By Jim Robinson
Hi, What version of IGV are you using? It...

Hi,

What version of IGV are you using? It should automatically recognize and alias identifiers of that sort.

I'm sure there are more direct ways to do this, but this method works. First cut...
Forum: Bioinformatics 11-24-2012, 05:23 PM
Replies: 11
Views: 14,472
Posted By Jim Robinson
I'm pretty late to this thread, missed the...

I'm pretty late to this thread, missed the original post. However, for the record IGV displays blat output in the form of .psl files, the extension must be .psl. There's no need to convert it to...
Forum: Bioinformatics 09-26-2012, 06:29 AM
Replies: 7
Views: 2,115
Posted By Jim Robinson
Hi, Could you contact us at...

Hi,

Could you contact us at igv-team@broadinstitute.org? We can arrange to maybe transfer your reference genome and a test file.

Also, the new early access version of IGV should not return...
Forum: Bioinformatics 09-25-2012, 02:54 AM
Replies: 7
Views: 2,115
Posted By Jim Robinson
Hi, this looks like an IGV bug (obviously). I...

Hi, this looks like an IGV bug (obviously). I am trying to reproduce it, in the meantime could you try the "early access" version to see if the bug is fixed there, if not please send or post the...
Forum: Bioinformatics 09-11-2012, 04:29 AM
Replies: 1
Views: 983
Posted By Jim Robinson
You should be able to build such a program using...

You should be able to build such a program using the Sam JDK in the Picard package. It would be straightforward, there are examples in the form of unit tests. You want to open a SAMFileReader, ...
Forum: Bioinformatics 09-05-2012, 07:15 AM
Replies: 11
Views: 2,930
Posted By Jim Robinson
You can use igvtools to compute coverage from a...

You can use igvtools to compute coverage from a bed file. I think bedtools can also do this.
Forum: Bioinformatics 08-31-2012, 04:23 AM
Replies: 3
Views: 4,311
Posted By Jim Robinson
Hi, Could you elaborate on where you have...

Hi,

Could you elaborate on where you have found differences in chromsome "Y"s sequence? These should be identical between versions you mention.

-- Jim
Forum: Bioinformatics 08-09-2012, 07:02 AM
Replies: 18
Views: 14,822
Posted By Jim Robinson
red = neg strand (first read of the pair is no...

red = neg strand (first read of the pair is no the neg strand)
blue = pos strand
grey = pair information not available, so "first of pair" is undefined
Forum: Bioinformatics 08-09-2012, 03:50 AM
Replies: 18
Views: 14,822
Posted By Jim Robinson
Hi, It depends on the library details, but...

Hi,

It depends on the library details, but you should could try "color by first-in-pair" from the popup menu. This will color by the strand of the template, rather than the read, at least for...
Forum: Bioinformatics 06-13-2012, 09:22 AM
Replies: 7
Views: 8,535
Posted By Jim Robinson
Hi, IGV is not making any judgement calls,...

Hi,

IGV is not making any judgement calls, is is using the mapping quality. It is a convention with at least some aligners (BWA), if not all aligners, that mapping quality == 0 means the read is...
Forum: Bioinformatics 05-17-2012, 07:05 PM
Replies: 1
Views: 1,706
Posted By Jim Robinson
Hi Philip, Sorry for the difficulties. We...

Hi Philip,

Sorry for the difficulties. We have had other reports of this, but sporadic. What I need is someone to work with me long enough to isolate the cause, we use it heavily here at the...
Forum: Bioinformatics 03-13-2012, 02:13 AM
Replies: 2
Views: 1,634
Posted By Jim Robinson
Hi, That will work, you can also use bed...

Hi,

That will work, you can also use bed format but you have to use the extended form. See the UCSC site for details. BED files have the advantage of being much smaller, in general, and can...
Forum: Bioinformatics 03-11-2012, 05:38 AM
Replies: 1
Views: 1,062
Posted By Jim Robinson
Hi tia, If your chromosome names are of the...

Hi tia,

If your chromosome names are of the form "chr1, chr2, chr3, ..." etc, you can download the following file from UCSC and just load it using "File > Load..." after selecting you custom...
Forum: Bioinformatics 02-20-2012, 11:15 PM
Replies: 2
Views: 2,393
Posted By Jim Robinson
Actually if you download the gzipped (tabix) file...

Actually if you download the gzipped (tabix) file and the index (...gz.tbi) you don't need to do anything, just load it. I'm assuming these files are tabix-indexed.

Also, you can actually load...
Forum: Bioinformatics 02-11-2012, 07:34 AM
Replies: 2
Views: 3,997
Posted By Jim Robinson
Hi, First IGV has a help forum where you are...

Hi,

First IGV has a help forum where you are more likely to get a timely response, the URL is https://groups.google.com/forum/?hl=en_US#!forum/igv-help

A couple of points (1) you don't need...
Forum: General 02-02-2012, 06:27 AM
Replies: 4
Views: 4,287
Posted By Jim Robinson
Sure, to emphasize this only works for indexed...

Sure, to emphasize this only works for indexed fastas. You can index them with samtools.
Forum: General 02-02-2012, 05:55 AM
Replies: 4
Views: 4,287
Posted By Jim Robinson
Hi Keo, I've looked at your problem and logs...

Hi Keo,

I've looked at your problem and logs a little more, and for the sake of others who might search this forum let me clarify. I think your problem stemmed from trying to move the .genome...
Showing results 1 to 25 of 75

 


All times are GMT -8. The time now is 11:14 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO