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Forum: General 01-01-2018, 06:49 PM
Replies: 2
Views: 1,353
Posted By Heisman
Thanks a bunch! I really appreciate it.

Thanks a bunch! I really appreciate it.
Forum: General 12-31-2017, 08:54 AM
Replies: 2
Views: 1,353
Posted By Heisman
What is the current state of sequencing?

Hey all,

It's been several years since I last logged in and several years since I've been involved in sequencing. I'm curious how things have progressed in the last handful of years. Is there any...
Forum: Bioinformatics 11-17-2013, 02:14 PM
Replies: 3
Views: 1,537
Posted By Heisman
I looked into this once and didn't find anything,...

I looked into this once and didn't find anything, although there could definitely be something out there. What I ended up doing was getting the bed coordinates from each read, extending them by...
Forum: Bioinformatics 11-05-2013, 06:31 AM
Replies: 15
Views: 1,770
Posted By Heisman
I don't quite understand your question. Could you...

I don't quite understand your question. Could you provide the line of code you used to run bowtie? I use Bowtie2 and I believe when it's finished aligning it provides output stating how many reads...
Forum: Sample Prep / Library Generation 11-04-2013, 03:56 PM
Replies: 3
Views: 3,507
Posted By Heisman
What I did back in the day I was working on this...

What I did back in the day I was working on this was to make my own solution of PEG and NaCl and not use the bead solution. So, I'd put an aliquot of beads on a magnet, discard the entire...
Forum: Bioinformatics 10-28-2013, 08:40 AM
Replies: 3
Views: 1,691
Posted By Heisman
Another thought would be to try Picard. I do not...

Another thought would be to try Picard. I do not know if it is faster or not but it may be. It will handle headers more appropriately:...
Forum: General 10-15-2013, 06:14 AM
Replies: 4
Views: 2,392
Posted By Heisman
Excellent, thanks everyone.

Excellent, thanks everyone.
Forum: General 10-14-2013, 07:34 PM
Replies: 4
Views: 2,392
Posted By Heisman
Counting CpG's per read, please check my logic.

Simple question but I want to make sure I get this right. Basically I'm looking at pulldowns of regions enriched with methylated CpG's.

Let's say I have a read that has the sequence:...
Forum: Bioinformatics 09-08-2013, 06:51 PM
Replies: 4
Views: 1,684
Posted By Heisman
What book are you reading and what year was it...

What book are you reading and what year was it published? That is not an accurate statement, I don't think. The bottlenecks are usually either obtaining relevant clinical samples, obtaining sequence...
Forum: Introductions 09-06-2013, 05:15 PM
Replies: 5
Views: 2,645
Posted By Heisman
You didn't really ask a question. What exactly...

You didn't really ask a question. What exactly does your lab work on that would justify using RNA-seq? In terms of showing nice data I imagine you can use things already published and show how...
Forum: Bioinformatics 08-28-2013, 04:16 PM
Replies: 1
Views: 3,134
Posted By Heisman
Trying to install bedToBigBed, libssl.so.10 issue

Hey all,

When trying to use bedToBigBed, I get:

bedToBigBed: error while loading shared libraries: libssl.so.10: cannot open shared object file: No such file or directory

I have googled...
Forum: Bioinformatics 08-25-2013, 05:00 PM
Replies: 2
Views: 1,340
Posted By Heisman
I haven't used it in forever but it may be...

I haven't used it in forever but it may be keeping the old quality scores as well as the recalibrated ones. If that is default now there is an option to have it not do that (at least there was over a...
Forum: Genomic Resequencing 08-20-2013, 09:57 AM
Replies: 3
Views: 2,811
Posted By Heisman
Look into earray with agilent - custom capture....

Look into earray with agilent - custom capture. Won't be very cost-efficient for only one sample but if you have a decent amount it's one thing to look into for sure.
Forum: Bioinformatics 08-19-2013, 08:42 AM
Replies: 16
Views: 11,129
Posted By Heisman
Create a file with vim and then type the...

Create a file with vim and then type the following (with tabs):

chr1 500 1000
chr1 700 1200

and try to use "mergeBed" on it and see if that works.
Forum: Bioinformatics 08-11-2013, 06:41 PM
Replies: 12
Views: 11,217
Posted By Heisman
I think your next step is to try to figure out...

I think your next step is to try to figure out what's going on. I'd start with W1 and W2 as they seem to be horribly correlated but should be biological replicates.

So I would do a few things with...
Forum: Bioinformatics 08-10-2013, 06:12 AM
Replies: 5
Views: 1,102
Posted By Heisman
I have not used Somaticsniper, but many callers...

I have not used Somaticsniper, but many callers will allow you to specify a list of regions for which to call SNVs. Read through the manual perhaps and see if that's allowed. Otherwise, it depends on...
Forum: Bioinformatics 08-06-2013, 09:51 PM
Replies: 12
Views: 11,217
Posted By Heisman
What is your duplication rate? Even if you...

What is your duplication rate?

Even if you call no peaks, you can correlate overall signal as described in the link provided here:...
Forum: Bioinformatics 08-06-2013, 09:00 AM
Replies: 4
Views: 1,594
Posted By Heisman
Maybe others will have ideas, but if they are...

Maybe others will have ideas, but if they are exactly the same (ie, identical headers, bases, quality scores), you could convert them to one line, combine the files, sort them, and then use uniq, as...
Forum: General 08-04-2013, 07:10 PM
Replies: 4
Views: 5,622
Posted By Heisman
Thank you, I'm a new python user. School is...

Thank you, I'm a new python user. School is starting up for me tomorrow so it'll be a bit before I can look at this in more detail but I will do so within a week. Thank you very much for the feedback.
Forum: General 08-04-2013, 01:52 PM
Replies: 5
Views: 1,681
Posted By Heisman
If you google you may find this link:...

If you google you may find this link: http://unix.stackexchange.com/questions/18736/how-to-count-the-number-of-a-specific-character-in-each-line

Here's a bash script that will work. Run it as...
Forum: General 08-04-2013, 01:27 PM
Replies: 4
Views: 5,622
Posted By Heisman
I wrote an equivalent program in C++ and it works...

I wrote an equivalent program in C++ and it works in <5 seconds on my work computer, lol. Still have no idea what's going wrong with the python script. Sometimes I hate computers.
Forum: General 08-04-2013, 08:33 AM
Replies: 4
Views: 5,622
Posted By Heisman
python script running slowly, can't figure out why

Hey all,

If there is a better forum for this type of question, let me know; this is the only one I frequent currently but I can expand if necessary.

Anyways, the question itself is basic; to...
Forum: Bioinformatics 08-02-2013, 06:33 AM
Replies: 9
Views: 1,598
Posted By Heisman
As mastal said, you should; that's what I was...

As mastal said, you should; that's what I was alluding to above. Could you specify your restriction footprint as part of your adapter sequence? Would the footprint always be the same? If so that can...
Forum: Bioinformatics 08-01-2013, 11:08 AM
Replies: 6
Views: 2,815
Posted By Heisman
We need to have a mandatory sticky that should be...

We need to have a mandatory sticky that should be read and quizzed over prior to asking questions. Your post makes little sense to me. Please copy and paste all of the commands you used as well as...
Forum: Bioinformatics 08-01-2013, 07:44 AM
Replies: 9
Views: 1,598
Posted By Heisman
I don't know if you're willing to re-analyze...

I don't know if you're willing to re-analyze everything, but if you are you can specify cut adapt to get rid of reads that are 6bp or shorter. But again, if you have paired end reads you need to be...
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