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Forum: Oxford Nanopore 05-10-2018, 06:56 AM
Replies: 15
Views: 2,971
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: 231
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: 231
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: 207
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: 207
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: 174
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: 197
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: 197
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: 157
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: 157
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: 338
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: 476
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: 433
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: 367
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: 692
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: 692
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: 692
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: 692
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: 266
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: 203
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: 946
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: 121,392
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.
Forum: Illumina/Solexa 04-21-2018, 01:15 PM
Replies: 4
Views: 455
Posted By GenoMax
All new data should be phred+33. If you have data...

All new data should be phred+33. If you have data that is 5+ yr old then you have to worry about it being phred+33.
Forum: Illumina/Solexa 04-20-2018, 07:27 AM
Replies: 5
Views: 475
Posted By GenoMax
BBMap includes sequences of commonly used adapter...

BBMap includes sequences of commonly used adapter sequences (Illumina kits) in a file in BBMap software. Look for that file (adapters.fa) in "resources" directory of software distribution. You can...
Forum: Illumina/Solexa 04-19-2018, 05:00 PM
Replies: 5
Views: 475
Posted By GenoMax
You can't eyeball millions of reads. Use a...

You can't eyeball millions of reads. Use a program like bbduk (guide (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/)) and scan your files. If your data has no adapter...
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