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 Today, 09:35 AM
Replies: 1
Views: 36
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 Today, 09:24 AM
Replies: 1
Views: 3
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 Today, 09:17 AM
Replies: 1
Views: 37
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: 3,012
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: 246
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: 246
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: 220
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: 220
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: 188
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: 210
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: 210
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: 168
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: 168
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: 344
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: 484
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: 442
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: 377
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: 701
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: 701
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: 701
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...
Forum: RNA Sequencing 04-27-2018, 07:48 AM
Replies: 10
Views: 701
Posted By GenoMax
You made a "new" reference by appending the fasta...

You made a "new" reference by appending the fasta ERCC sequences to end of human genome and then created the STAR indexes from this hybrid file?
Forum: RNA Sequencing 04-26-2018, 03:39 AM
Replies: 1
Views: 277
Posted By GenoMax
Cross-posted: https://www.biostars.org/p/311462/

Cross-posted: https://www.biostars.org/p/311462/
Forum: Bioinformatics 04-25-2018, 05:26 AM
Replies: 1
Views: 210
Posted By GenoMax
Do you expect to see those poly-C and poly-T...

Do you expect to see those poly-C and poly-T stretches after ~106 position?
Forum: Illumina/Solexa 04-23-2018, 02:56 PM
Replies: 7
Views: 960
Posted By GenoMax
@nano85: I suggest that you actually calculate...

@nano85: I suggest that you actually calculate the insert sizes by using one of the methods noted by @Brian in post #2 here. (http://seqanswers.com/forums/showthread.php?t=73038)
Forum: Bioinformatics 04-23-2018, 03:48 AM
Replies: 636
Views: 121,669
Posted By GenoMax
Consider...

Consider http://seqanswers.com/forums/showthread.php?p=214346 (posts 204-206). BBMap does not seem to report ALL alignments in output file. @Brian may seen this and comment.
Showing results 1 to 25 of 500

 


All times are GMT -8. The time now is 09:46 AM.


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