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Search: Posts Made By: Marisa_Miller
Forum: Bioinformatics 02-26-2015, 08:47 AM
Replies: 0
Views: 533
Posted By Marisa_Miller
Undefined variants detected with SVDetect

Hi everyone,

I am just getting started using SVDetect and am having some trouble interpreting some strange results.

I am using mapped 300 bp PE reads (some are trimmed to less than 300 mp)...
Forum: Bioinformatics 02-12-2015, 01:39 PM
Replies: 17
Views: 3,977
Posted By Marisa_Miller
Thank you! Just tested the new version and it's...

Thank you! Just tested the new version and it's working now. And that makes sense about the "names" input. I will keep that in mind for the future.
Forum: Bioinformatics 02-12-2015, 11:31 AM
Replies: 17
Views: 3,977
Posted By Marisa_Miller
Sorry to bug you with another bug! I thought...

Sorry to bug you with another bug! I thought filterbyname.sh was working fine but I realized made an error in my command. Due to a typing error I was using a file that doesn't exist as my "names"...
Forum: Bioinformatics 02-12-2015, 05:41 AM
Replies: 17
Views: 3,977
Posted By Marisa_Miller
Hi Brian, I downloaded the new version and I...

Hi Brian,

I downloaded the new version and I was able to successfully filter out the mapped reads only.

When I try to get the intersection between the two files I am getting this error:
...
Forum: Bioinformatics 02-11-2015, 08:35 AM
Replies: 17
Views: 3,977
Posted By Marisa_Miller
Hi Brian, Thanks again for the help. I am...

Hi Brian,

Thanks again for the help. I am currently running the program now and it gave me an error message:

java -ea -Xmx200m -cp /home/kianians/millerm2/scripts/bbmap/current/...
Forum: Bioinformatics 02-10-2015, 01:18 PM
Replies: 17
Views: 3,977
Posted By Marisa_Miller
Compare mapped reads in SAM/BAM files

Hello,

I have two different SAM/BAM files for a sequenced library (Illumina library sequenced paired-end) which were generated by mapping the reads (with Bowtie2) to two different reference...
Forum: Bioinformatics 01-27-2015, 08:43 AM
Replies: 25
Views: 15,508
Posted By Marisa_Miller
Hi Brian, Does the subsampling tool randomly...

Hi Brian,

Does the subsampling tool randomly subsample reads? The program I am using now (Geneious) only takes the first specified % of reads and does not randomize.

Thank you,
Marisa
Forum: Bioinformatics 01-21-2015, 04:52 AM
Replies: 126
Views: 46,732
Posted By Marisa_Miller
Thanks Brian!

Thanks Brian!
Forum: Bioinformatics 01-20-2015, 01:58 PM
Replies: 126
Views: 46,732
Posted By Marisa_Miller
Hi Brian, I used BBmerge to merge my 2x300bp...

Hi Brian,

I used BBmerge to merge my 2x300bp reads last month, but now I need to determine the size distribution of my merged reads. Is there a way to do this with BBmerge? I know how to determine...
Forum: Bioinformatics 11-20-2014, 11:27 AM
Replies: 18
Views: 4,171
Posted By Marisa_Miller
I think I misunderstood earlier about what to...

I think I misunderstood earlier about what to look for in a library to see if it can be merged. I will go ahead and merge them and give the assembly a shot with both merged and unmerged. Thanks again!
Forum: Bioinformatics 11-20-2014, 11:09 AM
Replies: 18
Views: 4,171
Posted By Marisa_Miller
Hi Brian, I re-ran bbmerge with the correct...

Hi Brian,
I re-ran bbmerge with the correct command, and it looks like the distribution shows the insert sizes are too big for merging. Although, the fraction joined is around 60% for most...
Forum: Bioinformatics 11-20-2014, 08:00 AM
Replies: 18
Views: 4,171
Posted By Marisa_Miller
Hi Brian, Thanks for the useful information....

Hi Brian,
Thanks for the useful information. I quality trimmed the reads with a lower score limit (Q10) and did not specify a minimum read length.

I merged the reads with your program, and have...
Forum: Bioinformatics 11-19-2014, 06:14 AM
Replies: 18
Views: 4,171
Posted By Marisa_Miller
I do have a ridiculous amount of coverage, even...

I do have a ridiculous amount of coverage, even after trimming with a min length specified (~400X for most libraries), so perhaps some less stringent trimming will improve performance.
Forum: Bioinformatics 11-19-2014, 06:12 AM
Replies: 18
Views: 4,171
Posted By Marisa_Miller
Thanks for the suggestion, I will try both "raw...

Thanks for the suggestion, I will try both "raw data" and min length trimmed data for assembly to see what the results look like.
Forum: Bioinformatics 11-19-2014, 06:11 AM
Replies: 18
Views: 4,171
Posted By Marisa_Miller
These are the trimmomatic settings I was using...

These are the trimmomatic settings I was using ILLUMINACLIP:$TRIMMOMATIC/adapters/NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:250.

It seems like there aren't any...
Forum: Bioinformatics 11-18-2014, 01:57 PM
Replies: 18
Views: 4,171
Posted By Marisa_Miller
Below is the 6th file.

Below is the 6th file.
Forum: Bioinformatics 11-18-2014, 01:57 PM
Replies: 18
Views: 4,171
Posted By Marisa_Miller
I have posted the FastQC results for 2 different...

I have posted the FastQC results for 2 different libraries, #1 and #10. For each library, I have the FastQC results for the raw untrimmed data, quality trimmed data, and quality trimmed + 250 bp...
Forum: Bioinformatics 11-18-2014, 10:58 AM
Replies: 18
Views: 4,171
Posted By Marisa_Miller
Minimum length for read trimming

Hi everyone,
I will be performing de novo and reference guided assembly of mitochondrial genomes using Geneious, and have a question regarding the minimum recommended read length to trim my reads...
Forum: Bioinformatics 11-11-2014, 03:09 AM
Replies: 365
Views: 161,038
Posted By Marisa_Miller
Hi Gabriel, Thanks for the info! I will do as...

Hi Gabriel,
Thanks for the info! I will do as you suggest and see if I can overlap those sequences to find out what they are.

Thanks!
Forum: Bioinformatics 11-08-2014, 07:19 AM
Replies: 365
Views: 161,038
Posted By Marisa_Miller
I didn't realize that heptamers would be too...

I didn't realize that heptamers would be too short to blast. I have searched with a few full reads and they all come up as wheat or wheat wild relative mitochondrial or plastid sequence, which is...
Forum: Bioinformatics 11-07-2014, 12:00 PM
Replies: 365
Views: 161,038
Posted By Marisa_Miller
Hi Simon, Thanks so much for the information....

Hi Simon,
Thanks so much for the information. After mapping I will take a look at the coverage distribution to see if the bias is causing an issue. I'm just glad that the problem shouldn't...
Forum: Bioinformatics 11-07-2014, 11:57 AM
Replies: 365
Views: 161,038
Posted By Marisa_Miller
I tried blasting the short heptamers against the...

I tried blasting the short heptamers against the Nucleotide collection (nr/nt) database. Not sure why I don't get any hits back.
Forum: Bioinformatics 11-07-2014, 06:39 AM
Replies: 365
Views: 161,038
Posted By Marisa_Miller
Kmer overrepresentation and per base sequence content in Nextera XT libraries

Hi all,
After reading around on the forums and elsewhere on the internet, it seems like seeing weird results for Kmer overrepresentation and per base sequence content after running FastQC on...
Forum: Bioinformatics 10-28-2014, 02:13 PM
Replies: 1
Views: 1,068
Posted By Marisa_Miller
Bump! I'm hoping some assembly experts out there...

Bump! I'm hoping some assembly experts out there have some good advice!
Forum: Bioinformatics 10-24-2014, 08:56 AM
Replies: 1
Views: 1,068
Posted By Marisa_Miller
De Novo Assembly of Wheat Mitochondrial Genomes

Hi everyone,
I will soon be analyzing a large number of wheat and wheat wild relative mitochondrial genomes and wanted to get some advice on assembly and analysis here.

-Library type: Nextera...
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