SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 500
Search took 0.06 seconds.
Search: Posts Made By: GenoMax
Forum: Illumina/Solexa Yesterday, 04:48 PM
Replies: 6
Views: 82
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 Yesterday, 01:23 PM
Replies: 6
Views: 82
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 Yesterday, 12:59 PM
Replies: 6
Views: 82
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 Yesterday, 03:02 AM
Replies: 5
Views: 111
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: 111
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: 112
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.
Forum: Bioinformatics 05-22-2018, 09:24 AM
Replies: 5
Views: 111
Posted By GenoMax
That 10G is a guide (I assume you took that from...

That 10G is a guide (I assume you took that from the example command line). What size is your BAM file? You may need to assign more RAM for this job.
Forum: Bioinformatics 05-22-2018, 09:17 AM
Replies: 2
Views: 107
Posted By GenoMax
Curious why you want to do this. I don't know of...

Curious why you want to do this. I don't know of any software that will do this.
Forum: Oxford Nanopore 05-10-2018, 06:56 AM
Replies: 15
Views: 3,066
Posted By GenoMax
Perhaps you are using an unsupported linux distro?

Perhaps you are using an unsupported linux distro?
Forum: Bioinformatics 05-09-2018, 06:00 AM
Replies: 7
Views: 264
Posted By GenoMax
Tabix can accept these formats: -p gff|bed|sam|vcf

Tabix can accept these formats: -p gff|bed|sam|vcf
Forum: Bioinformatics 05-09-2018, 03:18 AM
Replies: 7
Views: 264
Posted By GenoMax
tabix (http://www.htslib.org/doc/tabix.html)from...

tabix (http://www.htslib.org/doc/tabix.html)from Samtools.
Forum: Illumina/Solexa 05-08-2018, 05:37 PM
Replies: 5
Views: 237
Posted By GenoMax
It must be the total frag size. Since the above...

It must be the total frag size. Since the above plot is post alignment it will correspond nicely to 150 bp inserts.
Forum: Illumina/Solexa 05-08-2018, 03:28 PM
Replies: 5
Views: 237
Posted By GenoMax
Can you tell us what aligner you used for this?...

Can you tell us what aligner you used for this? Is it possible that the aligner kept reads with reasonable distance (did you provide an expected fragment size) when mapping and discarded smaller...
Forum: Bioinformatics 05-07-2018, 02:59 PM
Replies: 2
Views: 194
Posted By GenoMax
Have you tried BBMerge to see if there are some...

Have you tried BBMerge to see if there are some reads that can merge (have insert sizes smaller than expected).

You could try bbmerge.sh's tadpole "extend "modes to see if you are able to...
Forum: Bioinformatics 05-07-2018, 10:52 AM
Replies: 3
Views: 215
Posted By GenoMax
You should align the data without doing any...

You should align the data without doing any additional manipulations beyond removal of adapters. Data should align normally.
Forum: Bioinformatics 05-07-2018, 10:22 AM
Replies: 3
Views: 215
Posted By GenoMax
Have you come across this blog post...

Have you come across this blog post (https://sequencing.qcfail.com/articles/positional-sequence-bias-in-random-primed-libraries/)?

What you are observing is the "bias" observed similar to random...
Forum: Bioinformatics 05-07-2018, 08:57 AM
Replies: 3
Views: 176
Posted By GenoMax
Good to know that bbduk worked. When you want to...

Good to know that bbduk worked. When you want to collect something that matches outm= is the way to go.
Forum: Bioinformatics 05-07-2018, 02:58 AM
Replies: 3
Views: 176
Posted By GenoMax
I believe that Geneious may actually be using...

I believe that Geneious may actually be using `bbduk.sh` from BBMap internally. Have you tried that program?
Forum: Bioinformatics 05-03-2018, 03:47 AM
Replies: 1
Views: 346
Posted By GenoMax
Cross-posted: https://www.biostars.org/p/312889/

Cross-posted: https://www.biostars.org/p/312889/
Forum: Bioinformatics 04-30-2018, 04:18 AM
Replies: 1
Views: 487
Posted By GenoMax
For reference cross-posted to biostars:...

For reference cross-posted to biostars: https://www.biostars.org/p/312195/
Forum: Bioinformatics 04-29-2018, 03:54 PM
Replies: 1
Views: 444
Posted By GenoMax
Cross-posted on Biostars:...

Cross-posted on Biostars: https://www.biostars.org/p/312084/
Forum: RNA Sequencing 04-29-2018, 03:49 PM
Replies: 1
Views: 387
Posted By GenoMax
No. Some duplication is expected in RNAseq (based...

No. Some duplication is expected in RNAseq (based on your posts on Biostars).
Forum: RNA Sequencing 04-27-2018, 11:58 AM
Replies: 10
Views: 710
Posted By GenoMax
Can you try featureCounts ...

Can you try featureCounts (http://bioinf.wehi.edu.au/featureCounts/)to do the counts? It will not count multi-mapping reads by default.
Forum: RNA Sequencing 04-27-2018, 10:44 AM
Replies: 10
Views: 710
Posted By GenoMax
When you added them to the GTF file they were in...

When you added them to the GTF file they were in the correct format?

Are you able to see alignments for them in the BAM file?
Forum: RNA Sequencing 04-27-2018, 09:12 AM
Replies: 10
Views: 710
Posted By GenoMax
Then I am inclined to speculate that someone...

Then I am inclined to speculate that someone forgot to spike the ERCC aliquots. Unless alignments are not being reported since they fail STAR's multi-mapping threshold. Look into that as well.

Did...
Showing results 1 to 25 of 500

 


All times are GMT -8. The time now is 01:47 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO