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Search: Posts Made By: JenBarb
Forum: Bioinformatics 08-15-2018, 09:45 AM
Replies: 674
Views: 172,752
Posted By JenBarb
mkf argument in bbduk.sh (bbmap tool)

Hello,
I am trying to use the flag mkf (minkmerfraction) and I am getting an error that that argument does not exist.
sh /data/barbj/bbmap/bbduk.sh in=./../Stool_001-01.fastq outm=v2fstoolfq.fa...
Forum: Bioinformatics 08-09-2018, 07:09 AM
Replies: 674
Views: 172,752
Posted By JenBarb
Thank you! Love the tool!

Thank you! Love the tool!
Forum: Bioinformatics 08-09-2018, 05:56 AM
Replies: 674
Views: 172,752
Posted By JenBarb
pull out sequences with matching primers

Hi Brian,
I was wondering if bbmap has a tool that will pull out reads matching a particular primer sequences? I have fastq files with amplicons from 12 different primers in the same file so i want...
Forum: Bioinformatics 05-25-2018, 07:29 AM
Replies: 62
Views: 27,402
Posted By JenBarb
Is your tool suitable for microbiome data where...

Is your tool suitable for microbiome data where the database reference is many many bacterial 16s sequences?
i am looking for a tool that will take my fastq reads and align them to a given...
Forum: Bioinformatics 04-09-2018, 10:00 AM
Replies: 674
Views: 172,752
Posted By JenBarb
filterbyname.sh is not pulling out reads

Hello,
Any suggestions as to why filterbyname is not pulling out reads that I know are there.

Help??

Jen
Forum: Bioinformatics 12-15-2017, 08:10 AM
Replies: 3
Views: 849
Posted By JenBarb
Thank you. Blast at zfin does not seem to work...

Thank you. Blast at zfin does not seem to work with such short sequences so i am looking for other options or suggestions to this question.
Forum: Bioinformatics 12-15-2017, 07:51 AM
Replies: 3
Views: 849
Posted By JenBarb
miRNA seed sequence to target zebrafish genome

Hello,
Does anyone have any advice on how I can take a 7mer seed sequence of about 500 miRNAs and run a blast on all zebrafish genes in order to find perfect hits throughout the gene (not just in...
Forum: Bioinformatics 05-27-2015, 05:54 AM
Replies: 7
Views: 1,657
Posted By JenBarb
Hi Brian, How should I cite your tool in a...

Hi Brian,
How should I cite your tool in a manuscript in prep that I am doing? Do you have a reference or should I use your website?
Thanks,
Jen
Forum: Ion Torrent 05-06-2015, 09:25 AM
Replies: 11
Views: 9,198
Posted By JenBarb
Hello Jade, Did you end up making a decision to...

Hello Jade,
Did you end up making a decision to use the 16s kit or did you go with something else? If you did use the kit, I was just wondering how your progress with it is coming along?

Thanks,...
Forum: Metagenomics 03-17-2015, 05:38 AM
Replies: 1
Views: 1,161
Posted By JenBarb
Comparing OTUs from different V regions?

Hello,
I have data generated from using 6 different primers which target 6 different V regions of the 16s gene from the same samples. I am wondering if anyone has any advice on how to compare or...
Forum: RNA Sequencing 03-02-2015, 07:42 AM
Replies: 26
Views: 4,195
Posted By JenBarb
Hi Brian, I was talking about the...

Hi Brian,
I was talking about the filterbyname.sh script. However, I just did a sanity check on a subset and it worked. Then I reran it on the full data set and it worked. Maybe I was just too...
Forum: RNA Sequencing 02-27-2015, 11:21 AM
Replies: 26
Views: 4,195
Posted By JenBarb
Another question, Brian. Have you ever seen a...

Another question, Brian. Have you ever seen a case where the reformat.sh script did not work properly? I have made 4 subsets of read ids into name files from a large fasta file and I am trying to...
Forum: RNA Sequencing 02-27-2015, 07:03 AM
Replies: 26
Views: 4,195
Posted By JenBarb
Yes another awesome script! Thank you so much. ...

Yes another awesome script!
Thank you so much. If we ever get to publication, we will certain cite your tool!
jen
Forum: RNA Sequencing 02-26-2015, 07:23 AM
Replies: 26
Views: 4,195
Posted By JenBarb
Hi again Brian, Apparently you have all of the...

Hi again Brian,
Apparently you have all of the tools that I need for this problem that I am dealing with in my data. Now I am wondering if you have a tool that will extract a random subset of reads...
Forum: RNA Sequencing 02-24-2015, 09:16 AM
Replies: 26
Views: 4,195
Posted By JenBarb
Wonderful! I will try it. These tools are...

Wonderful! I will try it. These tools are amazing!
Jen
Forum: RNA Sequencing 02-24-2015, 07:43 AM
Replies: 26
Views: 4,195
Posted By JenBarb
Hello Again, I thought I would ask you a follow...

Hello Again,
I thought I would ask you a follow up question since you had a tool that nicely worked for my other issues. Do you have a script that will pull out reads that match a certain sequence...
Forum: RNA Sequencing 02-09-2015, 11:35 AM
Replies: 26
Views: 4,195
Posted By JenBarb
Thank you! It worked beautifully.

Thank you! It worked beautifully.
Forum: RNA Sequencing 02-09-2015, 10:57 AM
Replies: 26
Views: 4,195
Posted By JenBarb
Thank you again, Brian and GenoMax for all of...

Thank you again, Brian and GenoMax for all of your help.

I now am trying the filterbyname script and it does not seem to be pulling out only those reads that match a particular read id found in...
Forum: RNA Sequencing 02-09-2015, 09:50 AM
Replies: 26
Views: 4,195
Posted By JenBarb
Thank you so much for your help!

Thank you so much for your help!
Forum: RNA Sequencing 02-09-2015, 07:01 AM
Replies: 26
Views: 4,195
Posted By JenBarb
Hello again, So I tried the reformat.sh script...

Hello again,
So I tried the reformat.sh script on my fastq file. I then took each separate output file (fwd and reverse reads) and blasted the reads along a database of interest and am still...
Forum: RNA Sequencing 02-09-2015, 05:06 AM
Replies: 26
Views: 4,195
Posted By JenBarb
Thank you!!

Thank you!!
Forum: RNA Sequencing 02-09-2015, 04:57 AM
Replies: 26
Views: 4,195
Posted By JenBarb
Hi Brian, I am looking for the installation...

Hi Brian,
I am looking for the installation instructions on the page you sent and I can't find them. I also was looking for info about the two scripts that you sent. Is there a documentation page...
Forum: RNA Sequencing 02-06-2015, 12:01 PM
Replies: 26
Views: 4,195
Posted By JenBarb
Thank you so much for a quick reply! I really...

Thank you so much for a quick reply! I really appreciate it. I will try it now.
Jennifer
Forum: RNA Sequencing 02-06-2015, 11:39 AM
Replies: 26
Views: 4,195
Posted By JenBarb
extract forward and reverse reads?

Hello,
I have forward and reverse reads in a fastq file from Ion Torrent PGM sequencing data and I would like to know if anyone knows a way that I can extract the forward and reverse reads into two...
Forum: Ion Torrent 01-29-2015, 06:57 AM
Replies: 11
Views: 9,198
Posted By JenBarb
Hello Nabeeh, Have you made any progress with...

Hello Nabeeh,
Have you made any progress with this kit?
Jennifer
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