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Search: Posts Made By: sdriscoll
Forum: Bioinformatics 01-24-2018, 12:31 PM
Replies: 240
Views: 88,700
Posted By sdriscoll
Yeah I've come to terms with the fact that BBMap...

Yeah I've come to terms with the fact that BBMap wasn't really designed for this type of use. When I want to work with an alignment strategy where the goal is to find "all" alignments of a read up to...
Forum: RNA Sequencing 01-23-2018, 01:04 PM
Replies: 5
Views: 1,803
Posted By sdriscoll
What you're probably concerned with is if you can...

What you're probably concerned with is if you can rely on differential expression results from a small sample size such as 2 vs 3. The differential expression tools (DESeq2, edgeR, etc..) have very...
Forum: Bioinformatics 01-23-2018, 12:46 PM
Replies: 240
Views: 88,700
Posted By sdriscoll
@milan.molbio- bbmap looks for the best...

@milan.molbio-

bbmap looks for the best alignment and reports only that one by default. If there are multiple "best" then you can get them all by setting 'ambig=all'.

What you're looking for...
Forum: Bioinformatics 01-22-2018, 01:57 PM
Replies: 240
Views: 88,700
Posted By sdriscoll
Hello- I'm trying to understand this example...

Hello-

I'm trying to understand this example in the original post:


bbmap.sh in=reads.fq outu=unmapped.fq int=f
repair.sh in=unmapped.fq out=paired.fq fint outs=singletons.fq


It is...
Forum: Bioinformatics 01-17-2018, 10:47 AM
Replies: 9
Views: 13,497
Posted By sdriscoll
I kinda take issue with both approaches. With...

I kinda take issue with both approaches. With alignment to genome I always miss some alignments because aligning RNA-Seq to the genome is relatively difficult. STAR misses some alignments that GSNAP...
Forum: Bioinformatics 01-11-2018, 03:53 PM
Replies: 676
Views: 176,611
Posted By sdriscoll
mcmc- what are you setting the idfilter value to?...

mcmc- what are you setting the idfilter value to? Because reads still take a hit to their alignment score for soft-clipping. That is to say a read that's aligned with no mismatches but it was...
Forum: RNA Sequencing 01-11-2018, 03:22 PM
Replies: 1
Views: 1,636
Posted By sdriscoll
This locus looks like it has pretty low read...

This locus looks like it has pretty low read coverage based on the very blocky looking pileup. I'll say that a lot erratic coverage results from low read depth at a locus. Also if this is your first...
Forum: RNA Sequencing 01-11-2018, 02:15 PM
Replies: 1
Views: 2,083
Posted By sdriscoll
I don't know any articles but it sounds to me...

I don't know any articles but it sounds to me like you're going to have to use these steps:
1. use the WGS to assemble the genome
2. align RNA-Seq to the assembled genome using an RNA-Seq aligner...
Forum: RNA Sequencing 01-11-2018, 02:07 PM
Replies: 2
Views: 1,925
Posted By sdriscoll
The raw p-values in your results are still what...

The raw p-values in your results are still what they are - at a per-gene level given the dispersion models of the expression values in conditions that gene has a low probability of NOT being...
Forum: RNA Sequencing 01-11-2018, 01:51 PM
Replies: 1
Views: 2,242
Posted By sdriscoll
You may want to just split the data up into...

You may want to just split the data up into per-stimulation chunks. Otherwise the modeling in DESeq2 will use all samples and all stimulations to establish dispersions. If the separate stimulations...
Forum: RNA Sequencing 01-11-2018, 01:44 PM
Replies: 1
Views: 2,145
Posted By sdriscoll
I'm interpreting your meaning of "transcript...

I'm interpreting your meaning of "transcript counts" to be the expression levels of transcripts. You're correct that those do appear in the individual assemblies however after merging, since the...
Forum: RNA Sequencing 01-10-2018, 01:43 PM
Replies: 1
Views: 2,533
Posted By sdriscoll
Hi Jon, Not sure if you're still after any...

Hi Jon,

Not sure if you're still after any kind of answer but I can contribute a little bit of experience that may help guide you.

Q1: sure it is!

Q2:

Not necessarily. Direct to...
Forum: Bioinformatics 01-10-2018, 12:41 PM
Replies: 1
Views: 1,473
Posted By sdriscoll
I'd agree with that whereas if you were...

I'd agree with that whereas if you were interested in GO enrichment of the 15,000 genes you'd then use the 70,000 as the background.
Forum: Bioinformatics 01-10-2018, 12:25 PM
Replies: 2
Views: 2,140
Posted By sdriscoll
I sometimes use bowtie2 for the alignment stage...

I sometimes use bowtie2 for the alignment stage of running RSEM (RNA-Seq gene expression). RSEM didn't allow INDELS in the alignments so as part of tweaking bowtie2 to not report those I was advised...
Forum: Bioinformatics 01-10-2018, 10:17 AM
Replies: 0
Views: 524
Posted By sdriscoll
Is finding "all" alignments a pipe dream?

All is a bit arbitrary, of course, so maybe I just mean "all within a certain alignment quality boundary". I've wrestled with this time and time again - it seems that no matter how I tweak an...
Forum: Bioinformatics 04-27-2017, 10:08 AM
Replies: 676
Views: 176,611
Posted By sdriscoll
Oh yes! Thanks Brian.

Oh yes! Thanks Brian.
Forum: Bioinformatics 04-27-2017, 12:18 AM
Replies: 2
Views: 961
Posted By sdriscoll
first of all let me say that I agree with your...

first of all let me say that I agree with your interpretation. the third transcript does not overlap the first two and it has given all three the same 'gene_id' value.

the only thing that comes...
Forum: RNA Sequencing 04-27-2017, 12:07 AM
Replies: 6
Views: 4,716
Posted By sdriscoll
farri- Converting FPKM to TPM has zero...

farri-

Converting FPKM to TPM has zero effect on whatever careful way cufflinks calculated those FPKM values. It's actually not the FPKM that's carefully calculated within cufflinks but the...
Forum: RNA Sequencing 04-26-2017, 11:52 PM
Replies: 6
Views: 4,716
Posted By sdriscoll
I know this was cleared up in the post following...

I know this was cleared up in the post following it but I should correct you in that TPM is transcript length normalized just as FPKM. As pointed out the two are related by a constant factor, X. TPM...
Forum: Bioinformatics 04-26-2017, 11:42 PM
Replies: 0
Views: 952
Posted By sdriscoll
Uninterpretable behavior of Hisat2 with '-k' option

I just wanted to put this out here. I'm doing some work with simulated reads and it happens to matter when a read doesn't align which led me to look closely at the output of Hisat2 today. First...
Forum: Bioinformatics 04-26-2017, 10:43 PM
Replies: 676
Views: 176,611
Posted By sdriscoll
I was testing something with BBMap today and I...

I was testing something with BBMap today and I realized I had forgotten something about how to use it and couldn't figure it out. I was mapping RNA-Seq and I thought that it would report spliced...
Forum: Epigenetics 12-10-2015, 07:29 AM
Replies: 3
Views: 4,939
Posted By sdriscoll
MACS or Homer. Homer has a few peak calling modes...

MACS or Homer. Homer has a few peak calling modes that control the type and size of peaks it finds. MACS is more of a straight ahead peak caller that just looks for peaks of any width. at least...
Forum: Bioinformatics 07-23-2015, 12:56 PM
Replies: 104
Views: 32,933
Posted By sdriscoll
How does Tadpole compare to a short read...

How does Tadpole compare to a short read assembler such as Trinity? Is the output of Tadpole more like the results of the inchworm stage of the Trinity pipeline?

I tried Tadpole out on some...
Forum: Bioinformatics 07-21-2015, 03:49 PM
Replies: 676
Views: 176,611
Posted By sdriscoll
By the way this was when I had ambig=all and...

By the way this was when I had ambig=all and aligning PE reads. The odd behavior didn't seem to care whether or not I had 'secondary=t' set.
Forum: Bioinformatics 07-21-2015, 11:57 AM
Replies: 5
Views: 2,565
Posted By sdriscoll
Since it wasn't mentioned yet I'll add that...

Since it wasn't mentioned yet I'll add that cufflinks determines the strand of the assembled isoforms from the value of the XS attribute in the alignments (generated by STAR with --outSAMstrandField...
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