SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 70
Search took 0.01 seconds.
Search: Posts Made By: lwhitmore
Forum: Bioinformatics 03-19-2016, 02:01 PM
Replies: 3
Views: 1,522
Posted By lwhitmore
right so if we know that we have strand reversed...

right so if we know that we have strand reversed library and we use the option -s reverse then reads will only be counted if they map to the apposing strand that the feature "gene" is actually on...
Forum: Bioinformatics 03-18-2016, 11:11 AM
Replies: 3
Views: 1,522
Posted By lwhitmore
-s=reverse HTSEQ option

Hi,
When using the -s=reverse option for HTSEQ most reads counted are mapped to anti-sense strand of the gene. How does this option work and what exactly is it doing?

Thanks,
Leanne
Forum: Bioinformatics 03-17-2016, 12:20 PM
Replies: 1
Views: 1,083
Posted By lwhitmore
NEB kit E6120S

Hi,
I am analyzing data produced from a NEB kit E6120S kit and am wondering if this kit is suppose to be stranded or not? Additionally, if it is stranded is second-strand synthesis, meaning that...
Forum: Bioinformatics 03-04-2016, 05:31 PM
Replies: 0
Views: 962
Posted By lwhitmore
Script Seq mRNA-seq Library prep kit

Hi,
I have data produced from the ScriptSeq mRNA-seq library prep kit and I just want to check that reads produced from this kit should be complement to the transcript and for analyzing the gene...
Forum: Bioinformatics 03-04-2016, 04:26 PM
Replies: 6
Views: 1,939
Posted By lwhitmore
Thanks dpryan! I do have another question if...

Thanks dpryan!

I do have another question if multiple alignments is specified in the bowtie alignment (-a) will infer_experiment be able to work correctly in predicting strandedness?
Forum: Bioinformatics 02-12-2016, 01:07 PM
Replies: 6
Views: 1,939
Posted By lwhitmore
Thanks guys! this was very helpful! The paper...

Thanks guys! this was very helpful! The paper says an Illumina TruSeq Stranded mRNA LT kit so based on what Michael said it is to be expected that the read are the reverse complement of the gene. ...
Forum: Bioinformatics 02-11-2016, 08:07 PM
Replies: 6
Views: 1,939
Posted By lwhitmore
RSeqQC infer_experiment strandedness

Hi,

I am using RSeqQC infer_experiment.py to look at whether or not a library is stranded and I got the following results:

This is SingleEnd Data
Fraction of reads failed to determine: 0.0242...
Forum: Bioinformatics 02-18-2015, 08:34 AM
Replies: 6
Views: 4,828
Posted By lwhitmore
Default bowtie

Hi I am just wondering if you run bowtie with -v 0 (meaning no mismatches are allowed in the alignment) and -a (meaning mulitple alignments are allowed) is the last column the number of times the...
Forum: RNA Sequencing 02-17-2015, 01:54 PM
Replies: 2
Views: 1,665
Posted By lwhitmore
RNA-seq Reproducibility analysis

Hey,
I have 3 RNA-seq biological replicates of which I want to assess the reproducibility between the 3 replicates. I am only planning on performing HTSeq and looking at the read counts for our...
Forum: Bioinformatics 01-28-2015, 11:26 AM
Replies: 0
Views: 990
Posted By lwhitmore
ENCODE IDR platform questions

To anyone who can answer my questions !

I am using the Irreproducibility Discovery Rate (IDR) framework from encode to evaluate the reproducibility between two chip-seq replicates. When running...
Forum: Bioinformatics 01-09-2015, 08:17 AM
Replies: 8
Views: 5,531
Posted By lwhitmore
Rory, I looked at the page you mentioned and...

Rory,
I looked at the page you mentioned and that program specifically says if you used macs14 that you should not use it to calculate the IDR. Do you know of any programs that can accurately...
Forum: Bioinformatics 12-09-2014, 07:33 AM
Replies: 8
Views: 5,531
Posted By lwhitmore
Hi, Unfortunately I did not ever get an answer...

Hi,
Unfortunately I did not ever get an answer to that question.

Sorry, If you end up finding out why you should let me know

Leanne
Forum: Bioinformatics 10-07-2014, 10:43 AM
Replies: 1
Views: 976
Posted By lwhitmore
MUSCLE Alignment Stats

Hey I posted previously on The Muscle Alignment thread but didn't get any response so I thought I would try a new thread. Does any one know how to output the percent identity for each alignment using...
Forum: Bioinformatics 10-06-2014, 09:35 PM
Replies: 9
Views: 5,888
Posted By lwhitmore
Does any one know how to output the percent...

Does any one know how to output the percent identity for each alignment using the MUSCLE command line?
Forum: Bioinformatics 08-20-2014, 08:45 AM
Replies: 4
Views: 2,538
Posted By lwhitmore
By any chance does anyone know if there is a way...

By any chance does anyone know if there is a way to convert mm9 chromosome coordinates to mm10 genome coordinates?

Thanks
Leanne
Forum: Bioinformatics 08-20-2014, 07:16 AM
Replies: 4
Views: 2,538
Posted By lwhitmore
Great thank you!

Great thank you!
Forum: Bioinformatics 08-19-2014, 05:41 PM
Replies: 4
Views: 2,538
Posted By lwhitmore
gtf file reverse complement coordinates

Hey All, I have a question about chromosomal coordinates and Htseq. If I wanted to see if reads mapped to the chromosome location 4544400:4559600 on chromosome 1 the gtf line for this would be ...
Forum: Bioinformatics 07-07-2014, 02:57 PM
Replies: 3
Views: 1,703
Posted By lwhitmore
5' end adapter contamination

Hey All, I just have a general question. I am dealing with reads generated from illumina and am seeing the 5' adapter in many reads. Why would this occur? would it be a result of mis-annealing of...
Forum: Bioinformatics 06-20-2014, 10:17 AM
Replies: 5
Views: 2,731
Posted By lwhitmore
Hey I got it , I guess I wasn't putting in the...

Hey I got it , I guess I wasn't putting in the coordinates correctly
Forum: Bioinformatics 06-20-2014, 09:45 AM
Replies: 5
Views: 2,731
Posted By lwhitmore
Hey when I try using the ensembl browser no...

Hey when I try using the ensembl browser no matter which option I choose the sequence that is outputted is on N's
Forum: Bioinformatics 06-19-2014, 09:19 AM
Replies: 5
Views: 2,731
Posted By lwhitmore
Bedtools fastafrombed output

Hey Everyone, I had a quick question about my bedtools fastafrombed output. When I get a sequence it contains both capital and lowercase letters. Does anyone know why it does this or what it...
Forum: Bioinformatics 06-13-2014, 11:35 AM
Replies: 2
Views: 4,575
Posted By lwhitmore
Thanks Alot!

Thanks Alot!
Forum: Bioinformatics 06-13-2014, 11:02 AM
Replies: 2
Views: 4,575
Posted By lwhitmore
Cuffdiff Error Unrecognized file type (bam file)

Hey All, Using the following command for cuffdiff I get the error
Error: cannot open file /home/yelab/leanne/Projects/Xu_RNASeq/F4_Alignment/LS/LS_XXM_AGG_THout/accepted_hits.bam for reading....
Forum: Bioinformatics 06-06-2014, 05:09 PM
Replies: 8
Views: 5,531
Posted By lwhitmore
MACS Chip Seq Biological Replicates

Hey All,
I have 2 biological replicates for a treatment chip seq experiment. When I analyze these 2 replicates independently (using MACS 1.4.2) I get about 3000 peaks identified for both...
Forum: Bioinformatics 05-16-2014, 02:52 PM
Replies: 0
Views: 835
Posted By lwhitmore
closestBed questions output file and range

Hey!

I am new to using the Bedtools software and I have a couple of questions.
First, when using Bedtools closest (closestBed) it outputs a file with many columns. Is there any documentation on...
Showing results 1 to 25 of 70

 


All times are GMT -8. The time now is 11:47 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO