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Forum: Bioinformatics 01-24-2017, 06:30 PM
Replies: 2
Views: 1,519
Posted By bbm
Thank you for your thoughts. I have downloaded a...

Thank you for your thoughts. I have downloaded a bed file of honey bee from UCSC and tested in R, but it's still not working. This bed file has all 12 columns.
The only difference is my bed file...
Forum: Bioinformatics 01-23-2017, 06:18 AM
Replies: 2
Views: 1,519
Posted By bbm
Problem with BED file in methylKit

Hello all!

I am using methylkit to analyze my methylation data in honey bees.
I have converted a reference genome annotation file (gff3 file) to a bed file, then I run
...
Forum: Epigenetics 09-12-2016, 08:53 AM
Replies: 1
Views: 3,022
Posted By bbm
Bismark methylation extractor output

Hello all,

I used the extractor function to get CpG counts.


bismark_methylation_extractor -p --no_overlap --bedGraph --counts --buffer_size 10G --cytosine_report --genome_folder genome.fa...
Forum: General 04-22-2016, 07:43 AM
Replies: 5
Views: 1,737
Posted By bbm
I have the same question....any answers?

I have the same question....any answers?
Forum: Bioinformatics 03-10-2016, 06:58 AM
Replies: 649
Views: 170,782
Posted By bbm
Hi Felix, I have four lanes of data for each...

Hi Felix,

I have four lanes of data for each biological sample. Should I add them together before trimming and Bismark? Or is it better to do the trimming and Bismark run on the individual lane of...
Forum: Bioinformatics 03-07-2016, 01:35 PM
Replies: 649
Views: 170,782
Posted By bbm
I see, let me try

I see, let me try
Forum: Bioinformatics 03-07-2016, 01:20 PM
Replies: 649
Views: 170,782
Posted By bbm
I'm trying to do the genome conversion with this...

I'm trying to do the genome conversion with this line:

bismark_genome_preparation --bowtie2 --verbose /gpfs_share/hlibyar/hlibyar/genome_files/ --path_to_bowtie /usr/local/apps/bowtie2/


...
Forum: Bioinformatics 11-04-2015, 09:54 AM
Replies: 20
Views: 9,471
Posted By bbm
Anybody knows how to fix this? I ran into the...

Anybody knows how to fix this?
I ran into the same problem. I'm using cufflinks 2.2.1
Forum: Bioinformatics 10-07-2015, 02:58 PM
Replies: 2
Views: 946
Posted By bbm
Another related question here: My sequencing...

Another related question here:
My sequencing center said they didn't trimmed any adapters. So I went to the fastq.gz files, and grep the adapter sequence for the first 1 million reads, I only have...
Forum: Bioinformatics 10-07-2015, 02:36 PM
Replies: 2
Views: 946
Posted By bbm
cutadapt questions on pair-end seqeuencing data

I'm trying to use cutadapt to trim my data. The adaptor sequences from Illumina only has a universal adapter, then one sequence for each index.
Example here:
TruSeq Universal Adapter
5’...
Forum: RNA Sequencing 01-09-2015, 06:42 AM
Replies: 1
Views: 779
Posted By bbm
I also understand Tophat is splice-aware. My data...

I also understand Tophat is splice-aware. My data is transcriptome (mRNA), I expect Tophat to map at a similar rate to Bowtie. One difference is tophat maps reads that span splice junctions, right?
Forum: RNA Sequencing 01-09-2015, 06:39 AM
Replies: 34
Views: 4,591
Posted By bbm
any update from the OP? I'm have similar...

any update from the OP? I'm have similar problem...
Forum: RNA Sequencing 01-09-2015, 06:30 AM
Replies: 1
Views: 779
Posted By bbm
Different Results Of Tophat2 And Bowtie2

Hello all,

I ran the same fastq file with tophat2 and bowtie2, and got very different mapping rates. I wonder if any of you will help me on this puzzle. It is single-end, 60-100 bp after trimming....
Forum: RNA Sequencing 01-01-2015, 06:51 AM
Replies: 3
Views: 1,066
Posted By bbm
Thanks! I tried providing full path too, and have...

Thanks! I tried providing full path too, and have the same error.
The gff3 file is in current dir.
Forum: RNA Sequencing 01-01-2015, 05:28 AM
Replies: 3
Views: 1,066
Posted By bbm
tophat error with -G option

Hello all,

I'm trying to use tophat to run alignment.

Tophat version: tophat/2.0.12
Bowtie version: bowtie2/2.2.1

here is my command line for the job:
tophat -G amel_OGSv3.2.gff3...
Forum: Bioinformatics 10-27-2014, 04:51 AM
Replies: 12
Views: 1,805
Posted By bbm
The lib was done by the NEBNext® RNA Library Prep...

The lib was done by the NEBNext® RNA Library Prep Kit for Illumina, so it should be TruSeq adaptors.
Forum: Bioinformatics 10-27-2014, 04:50 AM
Replies: 12
Views: 1,805
Posted By bbm
The reference is honeybee genome, which is the...

The reference is honeybee genome, which is the 2nd version so far. Thank you for your suggestion. I think it may be the problem of low quality lib prep.
Forum: Bioinformatics 10-27-2014, 04:34 AM
Replies: 12
Views: 1,805
Posted By bbm
here is the overall fastqc

here is the overall fastqc
Forum: Bioinformatics 10-23-2014, 03:00 PM
Replies: 12
Views: 1,805
Posted By bbm
This is the fastqc after I trimmed using...

This is the fastqc after I trimmed using trimmomatic, 40-100bp

java -jar /usr/local/apps/trimmomatic/Trimmomatic-0.32/trimmomatic-0.32.jar SE 1.fastq 1.trimmed.fastq...
Forum: Bioinformatics 10-23-2014, 02:55 PM
Replies: 12
Views: 1,805
Posted By bbm
Attached here is the fastqc before I trimmed

Attached here is the fastqc before I trimmed
Forum: Bioinformatics 10-23-2014, 02:49 PM
Replies: 12
Views: 1,805
Posted By bbm
I just had no trimming data alignment, and it is...

I just had no trimming data alignment, and it is 15%.

15.66% overall alignment rate

I will post the fastqc plots soon. Thank you!
Forum: Bioinformatics 10-23-2014, 02:43 PM
Replies: 12
Views: 1,805
Posted By bbm
how to increase the mapping rate?

I have a set of RNA-seq dataset of single end 100bp reads (30 million per sample), and first using tophat2, mapping rate is only 5% to the ref genome. Then I tried to trim raw data to 40-100bp, and...
Forum: Bioinformatics 10-23-2014, 02:40 PM
Replies: 2
Views: 1,099
Posted By bbm
what do you mean of usedreads and unusedreads? ...

what do you mean of usedreads and unusedreads?
I'm learning how to use bowtie2 as well, and deal with single end data.
Forum: Bioinformatics 09-17-2014, 06:15 AM
Replies: 2
Views: 1,379
Posted By bbm
tophat job killed by run time limit

I got my tophat running, and then it was killed after a few minutes.


My output file said the job was killed after reaching LSF run time limit.
Exited with exit code 140.


This is the error...
Forum: Bioinformatics 09-12-2014, 05:57 AM
Replies: 33
Views: 5,255
Posted By bbm
Thanks! But my bowtie2 index are in the current...

Thanks! But my bowtie2 index are in the current dir?
still need to give the path?
I'll try that.
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