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Search: Posts Made By: GenoMax
Forum: Bioinformatics 06-22-2018, 03:02 AM
Replies: 1
Views: 351
Posted By GenoMax
Take a look at CD-HIT...

Take a look at CD-HIT (http://weizhongli-lab.org/cd-hit/).
Forum: Bioinformatics 06-21-2018, 06:21 AM
Replies: 2
Views: 272
Posted By GenoMax
NCBI requires use of API tokens with eUtils ...

NCBI requires use of API tokens with eUtils (https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/)as May 1st, 2018. It you are running a large amount of queries some of...
Forum: RNA Sequencing 06-20-2018, 01:50 PM
Replies: 2
Views: 458
Posted By GenoMax
Use bbsplit.sh from BBMap to separate human and...

Use bbsplit.sh from BBMap to separate human and mouse reads as shown in this thread (https://www.biostars.org/p/143019/#143040).

SeqAnswers thread page for BBsplit can be found here...
Forum: Illumina/Solexa 06-13-2018, 11:41 AM
Replies: 5
Views: 403
Posted By GenoMax
Good to know. We have a comparatively new machine...

Good to know. We have a comparatively new machine and have not used it a lot. S4 costs add up quickly, though you do get a ton of data.
Forum: Illumina/Solexa 06-13-2018, 05:03 AM
Replies: 5
Views: 403
Posted By GenoMax
We don't have a NextSeq in house so we have not...

We don't have a NextSeq in house so we have not done direct comparisons but as I understand it there are differences in NovaSeq chemistry (for better) compared to NextSeq (hard to find concrete info...
Forum: Bioinformatics 06-13-2018, 04:56 AM
Replies: 296
Views: 75,693
Posted By GenoMax
No hyphens. Just tpe and tbo.

No hyphens. Just tpe and tbo.
Forum: Bioinformatics 06-12-2018, 06:24 PM
Replies: 296
Views: 75,693
Posted By GenoMax
@horvathdp: You can provide NEBnext primers...

@horvathdp: You can provide NEBnext primers (https://www.neb.com/-/media/catalog/datacards-or-manuals/manuale7335.pdf) in a separate file as multi-fasta sequence. Then use that file with bbduk.sh....
Forum: Illumina/Solexa 06-12-2018, 06:19 PM
Replies: 5
Views: 403
Posted By GenoMax
Is there something specific you want to discuss?...

Is there something specific you want to discuss? NovaSeq works fine and is a workhorse. People in the lab like it since there is much less fuss with reagents etc. S4 FC's produce a ton of data. ~10B...
Forum: Bioinformatics 06-09-2018, 03:23 AM
Replies: 9
Views: 388
Posted By GenoMax
That is an "alpha" version (meaning a "work in...

That is an "alpha" version (meaning a "work in progress") of blast+. I would suggest not using that for any serious work. You should switch to the current shipping version. But as @Markian pointed...
Forum: Bioinformatics 06-08-2018, 05:11 AM
Replies: 9
Views: 388
Posted By GenoMax
Where did you get blast 2.8.0? Current version...

Where did you get blast 2.8.0? Current version available from NCBI's FTP site is v. 2.7.1.
Forum: Bioinformatics 06-08-2018, 05:09 AM
Replies: 7
Views: 320
Posted By GenoMax
Is this an assignment?

Is this an assignment?
Forum: Bioinformatics 06-08-2018, 04:17 AM
Replies: 7
Views: 320
Posted By GenoMax
Do you know how this file was generated? It...

Do you know how this file was generated?

It looks like this may actually be an aligned fasta format file so it would be not straight forward to identify how many duplicate sequences there were.
Forum: Core Facilities 06-07-2018, 09:47 AM
Replies: 3
Views: 334
Posted By GenoMax
Since those costs will vary from place to place...

Since those costs will vary from place to place even if you managed to get facilities to divulge that information it may not be of use.
Forum: RNA Sequencing 06-07-2018, 09:41 AM
Replies: 1
Views: 218
Posted By GenoMax
If you are using DESeq2/edgeR then they will...

If you are using DESeq2/edgeR then they will account for differences in the total number of reads. You could downsample the data to similar levels as an option.
Forum: Bioinformatics 06-01-2018, 09:26 AM
Replies: 60
Views: 16,308
Posted By GenoMax
@Priya: You should be able to include both...

@Priya: You should be able to include both sequences in the same command. There is always a debate about how to handle the multi-mapping (to both species) reads. First take a look to see how big that...
Forum: Illumina/Solexa 05-31-2018, 04:19 AM
Replies: 2
Views: 222
Posted By GenoMax
While bbmerge can be used to merge the reads in...

While bbmerge can be used to merge the reads in this case it will require the reference sequence since OP says:
Forum: Bioinformatics 05-30-2018, 02:54 PM
Replies: 2
Views: 244
Posted By GenoMax
Consider the answer given in this thread:...

Consider the answer given in this thread: https://www.biostars.org/p/289770/
Forum: Bioinformatics 05-25-2018, 07:45 AM
Replies: 60
Views: 16,308
Posted By GenoMax
BBsplit should work here. Make sure you clean...

BBsplit should work here. Make sure you clean fasta headers from your genome sequences (remove spaces in headers etc, make sure they are unique). You have the option of handling multi-mapping data in...
Forum: Bioinformatics 05-24-2018, 06:00 PM
Replies: 1
Views: 259
Posted By GenoMax
No. Unless the data is mapped to a reference you...

No. Unless the data is mapped to a reference you would not be able to determine the mapping percentage. The % will change depending on the reference you use and/or options you choose for the aligner....
Forum: Illumina/Solexa 05-23-2018, 04:48 PM
Replies: 6
Views: 292
Posted By GenoMax
Sure you can use trimmomatic. The options looks...

Sure you can use trimmomatic. The options looks right (I don't know them off the top of my head) and should work.
Forum: Illumina/Solexa 05-23-2018, 01:23 PM
Replies: 6
Views: 292
Posted By GenoMax
Context was the type of experiment. Sounds like...

Context was the type of experiment. Sounds like this is genome resequencing.

If you want to reduce possibility of reads multi-mapping by chance then going with longer reads is better. Minlen of 70...
Forum: Illumina/Solexa 05-23-2018, 12:59 PM
Replies: 6
Views: 292
Posted By GenoMax
Fails (red X) does not automatically mean your...

Fails (red X) does not automatically mean your data is bad. You need to take into account context of what kind of experiment this is. Can you tell us about that?

1. Aligners should soft-clip...
Forum: Bioinformatics 05-23-2018, 03:02 AM
Replies: 5
Views: 270
Posted By GenoMax
Ok. So it is your compiler that may be the...

Ok. So it is your compiler that may be the problem. What version of GCC did you use to compile this? You may need to use a newer version.
Forum: Bioinformatics 05-22-2018, 01:58 PM
Replies: 5
Views: 270
Posted By GenoMax
Have you run trinity with other data...

Have you run trinity with other data successfully? if not test it with something else. Did you compile the program yourself?
Forum: Illumina/Solexa 05-22-2018, 09:35 AM
Replies: 1
Views: 277
Posted By GenoMax
FastQC uses varying levels of data sampling (due...

FastQC uses varying levels of data sampling (due to time/memory constraints) to do various tests it presents. It is possible that could be the reason for the discrepancy you are noticing.
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