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Forum: Bioinformatics 09-03-2015, 04:10 PM
Replies: 4
Views: 1,145
Posted By bioBob
What is the opposite of TMI? Lots of things...

What is the opposite of TMI?

Lots of things can lead to issues in mapping. Sample degradation, sample contamination, etc. Seems to me that one of the things I would do is to get the reads that...
Forum: Bioinformatics 09-03-2015, 04:58 AM
Replies: 5
Views: 1,365
Posted By bioBob
Ahh, now you added new info, you have replicates...

Ahh, now you added new info, you have replicates AND a structure to your experiment. ;)

Yes, that would be ok.

If you had only a single sample AND the counts were from HTSeq, you could get...
Forum: Bioinformatics 09-03-2015, 04:25 AM
Replies: 5
Views: 1,365
Posted By bioBob
I should have stated, before you sort in R, make...

I should have stated, before you sort in R, make sure you have removed the bottom couple of rows.
Forum: Bioinformatics 09-03-2015, 04:13 AM
Replies: 5
Views: 1,365
Posted By bioBob
Hi, if you don't have a comparison, aka...

Hi,
if you don't have a comparison, aka differential expression, the DE part of DESeq2, I am not sure why you would go that route.

You have some other things to think about e.g. gene length and...
Forum: Bioinformatics 03-23-2015, 03:46 AM
Replies: 2
Views: 1,362
Posted By bioBob
Hi, thanks for the reply. That is the...

Hi,

thanks for the reply. That is the target id. From miRDB:

mmu-miR-669f-3p NM_001042565 99.7800236967459

I suppose I could get around the ensembl id's by using gene name, but I still...
Forum: Bioinformatics 03-21-2015, 11:09 AM
Replies: 2
Views: 1,362
Posted By bioBob
converting mirDB target ids to ensembl ids

Hi,

I have about 3000 miRNA targets from miRDB. I am needing to convert the target identifiers into Ensembl ids (mouse btw). About 2k of these convert using biomaRt in R. The other 1k I am not...
Forum: Bioinformatics 02-23-2015, 12:00 PM
Replies: 3
Views: 1,146
Posted By bioBob
DESeq2 paired plus condition

Hi,

I am having some trouble getting my head around it today, its Monday.

Essentially, I have a design matrix like so:

Patient Condition
58 2
58 3
64 2
Forum: Bioinformatics 02-05-2015, 04:45 AM
Replies: 7
Views: 2,418
Posted By bioBob
L-rna-scaffolder may also help. I have used...

L-rna-scaffolder may also help.

I have used it with varying success.
Forum: Bioinformatics 01-28-2015, 04:09 AM
Replies: 4
Views: 2,051
Posted By bioBob
I would check out MaSuRCA. As input, you would...

I would check out MaSuRCA. As input, you would give it the raw reads, not trimmed or stitched together. Each read set would be a unique library.

I have done this with a few different genomes...
Forum: Bioinformatics 01-26-2015, 05:37 PM
Replies: 1
Views: 1,181
Posted By bioBob
OK, figured it out. I should start my loop at 1,...

OK, figured it out. I should start my loop at 1, not 0. !!
Forum: Bioinformatics 01-26-2015, 05:24 PM
Replies: 2
Views: 1,222
Posted By bioBob
Plot the counts by replicate. Normalized.

Plot the counts by replicate. Normalized.
Forum: Bioinformatics 01-26-2015, 04:45 PM
Replies: 1
Views: 1,181
Posted By bioBob
parsing gff3 from NCBI

Hi,

I need some help parsing a gff3 file. Essentially, I am trying to pull out specific fields out of the info section using awk. I can't simply use the column arrangement because the lines do...
Forum: Bioinformatics 11-06-2014, 07:49 AM
Replies: 15
Views: 3,736
Posted By bioBob
My bad. I should always test code before...

My bad. I should always test code before posting.

Do:
awk '{x[$1]=x[$1]"\n"$2}END{for(j in x) print j,x[j]}' blast_file

You were correct, you could have added an if in there to get it as...
Forum: Bioinformatics 11-06-2014, 06:17 AM
Replies: 15
Views: 3,736
Posted By bioBob
Ok, easy enough. replace the "," in the awk with...

Ok, easy enough. replace the "," in the awk with "\n"

Not sure what you mean by pull fastas to the same line but the above should get you to the format you were hoping for. +/- an error in my...
Forum: Bioinformatics 11-06-2014, 05:51 AM
Replies: 15
Views: 3,736
Posted By bioBob
I think we are assuming you are at a linux...

I think we are assuming you are at a linux terminal.

If you have a blast table output file named blastOutput, to try to awk command I suggested type it out as
awk '{x[$1]=x[$1]","$2}END{for(j in...
Forum: Bioinformatics 11-04-2014, 05:12 AM
Replies: 15
Views: 3,736
Posted By bioBob
Hi, the chunking would save on compute time as I...

Hi, the chunking would save on compute time as I had thought that was your main issue.

What format do you need as input into your scripts?

query 1, hit 1, hit 2, ...
query 2, hit 1, hit 2,...
Forum: Bioinformatics 11-04-2014, 04:23 AM
Replies: 15
Views: 3,736
Posted By bioBob
I would echo rhinoceros' answer. Although I...

I would echo rhinoceros' answer. Although I would use tgicl and the cdbfasta/cdbyank programs. I would take your query fasta file, convert that to tab format, chunk your file into 200 subfiles...
Forum: Bioinformatics 11-04-2014, 04:17 AM
Replies: 2
Views: 742
Posted By bioBob
Hmm, I posted too quickly without having my first...

Hmm, I posted too quickly without having my first sip of coffee. It seems as though I need another check in there for feature. Which I now see is the reason you wanted to use groupBy.

Can you...
Forum: Bioinformatics 11-04-2014, 04:10 AM
Replies: 2
Views: 742
Posted By bioBob
Hi, it sounds like you are trying to do this...

Hi,

it sounds like you are trying to do this in R??

I will leave an R solution to someone with a bit more groupBy knowledge than me.

How about awk?

awk '{if($8>max8)...
Forum: Bioinformatics 09-05-2014, 03:42 AM
Replies: 2
Views: 871
Posted By bioBob
Hi, it might help to add some detail here. What...

Hi, it might help to add some detail here. What is the source of your data? NGS? What did you currently have, SNP and INDEL lists or it sounds like you have predicted gene sequences??
Forum: Bioinformatics 08-11-2014, 04:03 AM
Replies: 3
Views: 2,504
Posted By bioBob
They should be RF. That being said, there is...

They should be RF. That being said, there is generally significant contamination in MP libraries of PE. Check out NextClip and the Illumina technical bulletin on MP library analysis.
Forum: Bioinformatics 07-31-2014, 06:24 AM
Replies: 12
Views: 2,390
Posted By bioBob
Right, so you need to set that flag as the...

Right, so you need to set that flag as the default is name. You probably had a lot of messages in the console about mate not found.

-r <order>, --order=<order>
For paired-end data, the...
Forum: Bioinformatics 07-31-2014, 06:07 AM
Replies: 12
Views: 2,390
Posted By bioBob
Oh, and make sure the reads are sorted in the bam...

Oh, and make sure the reads are sorted in the bam file. HTSeq now has a flag for which method the sorting was performed, ie name or position.
Forum: Bioinformatics 07-31-2014, 05:56 AM
Replies: 12
Views: 2,390
Posted By bioBob
If it were me, I would align and count to the...

If it were me, I would align and count to the previous release just to see what the count assignments look like in terms of the number of reads in no_feature etc.

Another thing, are you sure the...
Forum: Bioinformatics 07-31-2014, 04:33 AM
Replies: 12
Views: 2,390
Posted By bioBob
No, that is not reasonable. Can you post a few...

No, that is not reasonable. Can you post a few lines of your corrected gtf?
Showing results 1 to 25 of 72

 


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