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Search: Posts Made By: kerhard
Forum: Bioinformatics 07-23-2013, 09:18 AM
Replies: 9
Views: 2,328
Posted By kerhard
Ah, I was guessing it might be the Perl rand()...

Ah, I was guessing it might be the Perl rand() function generating the coordinates, but wanted to be sure. Thanks very much!
Forum: Bioinformatics 07-22-2013, 10:29 PM
Replies: 9
Views: 2,328
Posted By kerhard
Hello, I'm using Sherman to generate sets of...

Hello,

I'm using Sherman to generate sets of 32 bp genomic sequences for use as random control "libraries" to some transcriptome libraries our lad has made. I compare the distribution of these...
Forum: Bioinformatics 05-31-2013, 12:38 PM
Replies: 26
Views: 3,747
Posted By kerhard
This is a great thread, I've been thinking about...

This is a great thread, I've been thinking about this issue for a while. I agree completely that biological replicates are the better way to go if it's feasible.

However, what about experiments...
Forum: Sample Prep / Library Generation 03-07-2013, 08:43 AM
Replies: 2
Views: 2,396
Posted By kerhard
Unfortunately, size is the main determination of...

Unfortunately, size is the main determination of my population of interest. If I were to make a library from this material, it would likely be strongly biased for miRNAs, which is not what I am...
Forum: Sample Prep / Library Generation 03-06-2013, 04:48 PM
Replies: 2
Views: 2,396
Posted By kerhard
Smaller than expected Bioanalyzer peak for size-selected RNAs?

Hello all,

I just got some strange Bioanalyzer results from their small RNA chip, was wondering if anyone had experienced anything similar. My intention is to make small RNA libraries from these...
Forum: Bioinformatics 11-08-2012, 06:34 PM
Replies: 11
Views: 14,656
Posted By kerhard
removing empty entries

In cutadapt, the program I used to remove adapter sequences from the reads, there is a parameter (-m, --minimum-length) that allows you to remove reads that are too short after removing the adapter. ...
Forum: Bioinformatics 08-17-2012, 10:18 AM
Replies: 11
Views: 14,656
Posted By kerhard
Yeah, I found out about that -Q parameter on...

Yeah, I found out about that -Q parameter on SEQanswers, it's "undocumented" in the Fastx toolkit. If the quality scores for your libraries are in the fastq sanger format (ascii(phred+33)), rather...
Forum: Bioinformatics 08-14-2012, 06:23 PM
Replies: 11
Views: 14,656
Posted By kerhard
Just wanted to add to this, as I got the same...

Just wanted to add to this, as I got the same error message from fastq_quality_filter, but I knew that I had the correct quality format because it worked on a differently processed version of the...
Forum: Bioinformatics 08-08-2012, 01:02 AM
Replies: 132
Views: 53,834
Posted By kerhard
Thanks for confirmation. I'm glad I tried out...

Thanks for confirmation. I'm glad I tried out cutadapt, as I was assuming my libraries were absent of adapter sequences, which turns out not to be true at all.

I suppose I still don't understand...
Forum: Bioinformatics 08-07-2012, 10:40 PM
Replies: 132
Views: 53,834
Posted By kerhard
Sorry, I wasn't reading the description of the...

Sorry, I wasn't reading the description of the options carefully enough. I think I understand now what the above results indicate. Using the -a option and given an adapter 21 bp in length, a longer...
Forum: Bioinformatics 08-07-2012, 08:22 PM
Replies: 132
Views: 53,834
Posted By kerhard
cutadapt trimming length issue

Hi all,

I just used cutadapt to process some libraries I made and got a result that I don't quite understand. It appears that cutadapt trimmed more than 21 bases (the length of the adapter...
Forum: General 04-19-2012, 10:54 PM
Replies: 1
Views: 2,171
Posted By kerhard
This depends on what you are planning to do with...

This depends on what you are planning to do with the data. If you are interested in comparing read counts between two libraries, you can't say much about non-unique reads with respect to a distinct...
Forum: Bioinformatics 04-21-2011, 11:50 AM
Replies: 514
Views: 221,464
Posted By kerhard
bowtie-index can use single fasta file with multiple entries as input

woops, didn't realize that the bowtie indexer could take a single fasta file with multiple entries as input. seems to work just fine that way. because the bowtie website describes the input for...
Forum: Bioinformatics 04-20-2011, 12:19 PM
Replies: 514
Views: 221,464
Posted By kerhard
Question limit to bowtie-build fasta input files?

Hi all,

I've been trying to make a bowtie index using a long list of annotated transposons as the input fasta files rather than reference chromosome files and bowtie-build does not seem to like it...
Forum: RNA Sequencing 04-18-2011, 02:26 PM
Replies: 5
Views: 3,158
Posted By kerhard
Has anyone been able to locate a maize GTF file...

Has anyone been able to locate a maize GTF file or create one from the GFF file from the Filtered Gene Set (http://ftp.maizesequence.org/current/filtered-set/)? Would be very useful.

To convert a...
Forum: RNA Sequencing 04-03-2011, 11:17 PM
Replies: 13
Views: 15,053
Posted By kerhard
Thanks! That makes a lot of sense now.

Thanks! That makes a lot of sense now.
Forum: RNA Sequencing 04-03-2011, 11:15 PM
Replies: 13
Views: 15,053
Posted By kerhard
Analyzing RNA-seq libraries with no replicates

Perusing the vignette for DESeq (mentioned above) by Simon Anders entitled "Analysing RNA-Seq data with the 'DESeq' package", I found this bit, which i think is quite informative and to the point:
...
Forum: Bioinformatics 04-03-2011, 08:22 PM
Replies: 70
Views: 59,555
Posted By kerhard
success

Right you were, I had named both of the data columns the same thing, woops. After fixing that, I was able to make a nice counts table for my data. So yes, your method is certainly applicable to...
Forum: RNA Sequencing 04-03-2011, 02:43 PM
Replies: 13
Views: 15,053
Posted By kerhard
Hi, I'm in the same boat (attempting to compare...

Hi, I'm in the same boat (attempting to compare two libraries without having replicates - they are similar to RNA-seq libraries) and am wondering whether this is going to be possible or not.


...
Forum: Bioinformatics 04-01-2011, 01:56 PM
Replies: 70
Views: 59,555
Posted By kerhard
more progress...

matching up the seq_name formatting between the bamfiles and the gff files definitely worked! i'm getting a data.frame that has something in it, so that's good.

however, when i try to generate...
Forum: Bioinformatics 03-31-2011, 03:44 PM
Replies: 70
Views: 59,555
Posted By kerhard
Ah, so if the seq_name formats must match between...

Ah, so if the seq_name formats must match between the two, then that is probably the issue.

here's what i get from head(my_bamfile@annotations):

seq_name strand inter_base...
Forum: Bioinformatics 03-31-2011, 02:27 PM
Replies: 70
Views: 59,555
Posted By kerhard
gff format in girafe / interval_overlap issues

I've identified what I think is a problem: I am getting ZERO overlaps between my aligned read intervals (from BAM file) and my annotation intervals from the interval_overlap function in girafe.
...
Forum: Bioinformatics 03-29-2011, 07:31 PM
Replies: 70
Views: 59,555
Posted By kerhard
ok, i was able to add the "family" and "class"...

ok, i was able to add the "family" and "class" columns to my gff file (I assume it doesn't matter whether the "family" column is called "ID" or "family")?

and to actually add something to this...
Forum: Bioinformatics 03-29-2011, 01:47 PM
Replies: 70
Views: 59,555
Posted By kerhard
ge_SF, thanks for the guide, i've been working up...

ge_SF, thanks for the guide, i've been working up from zero R familiarity, so it's taken me a bit of reading to get to this point...

the farthest i've gotten is trying to align my reads to my gff...
Forum: Bioinformatics 03-25-2011, 02:25 PM
Replies: 70
Views: 59,555
Posted By kerhard
non-model organisms & GenomicFeatures

Yes, this would be useful! Please post, it would be much appreciated. I'm working on libraries from maize, which is not on UCSC. Not sure exactly how I would change the maketranscriptDb function...
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