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Forum: Bioinformatics 02-11-2014, 01:48 AM
Replies: 7
Views: 1,749
Posted By roll
thank you dpryan

thank you dpryan
Forum: Bioinformatics 02-05-2014, 06:17 AM
Replies: 7
Views: 1,749
Posted By roll
i can't seem to find it in the iGenomes neither

i can't seem to find it in the iGenomes neither
Forum: Bioinformatics 02-05-2014, 04:43 AM
Replies: 5
Views: 4,585
Posted By roll
When i do the above, i tried to upload it to UCSC...

When i do the above, i tried to upload it to UCSC genome browser as custom track but it says it cant read my bigwig file.
I converted my bigwig to wig, this time it gives memory error.

Any ideas...
Forum: Bioinformatics 02-05-2014, 03:30 AM
Replies: 7
Views: 1,749
Posted By roll
thanks. i tried and it keeps giving me the...

thanks. i tried and it keeps giving me the following error

Can't start query:
describe rmsk

---------------------------------------------------------------------------...
Forum: Bioinformatics 02-05-2014, 02:52 AM
Replies: 7
Views: 1,749
Posted By roll
Tandem repeats in gff/gtf format

Hi,

I am trying to find tandem repeats (mainly SINE,LINE, ERV) position in gff/gtf format. I don't know if such files exist but i will be gratefull if you know such databases that I can download...
Forum: Bioinformatics 02-05-2014, 02:04 AM
Replies: 5
Views: 4,585
Posted By roll
This is chip-seq data and i used the following...

This is chip-seq data and i used the following commands

1. bedtools genomecov -bg -ibam Mysorted.bam > Mysorted.bedGraph

2. bedgraphToBigWig in.bedGraph chrom.sizes out.bw

At step 2, I am...
Forum: Bioinformatics 02-04-2014, 07:35 AM
Replies: 10
Views: 3,942
Posted By roll
i used featureCounts and used gff file from...

i used featureCounts and used gff file from mirBase. After selecting the right options, it returned me format i wanted it to be (count of each miRNA in each sample). Do you think, there is a mistake?
Forum: Bioinformatics 02-04-2014, 07:20 AM
Replies: 5
Views: 4,585
Posted By roll
How to convert sam/bam or bed file into wig file

Hi,

How what tools can I use to convert sam/bam or bed file into a wig file?
Forum: Bioinformatics 02-03-2014, 02:01 AM
Replies: 1
Views: 1,455
Posted By roll
what normalization should I do to compare featureCount outcome

I am using featureCount from Rsubread package. What normalization should I do after running the featureCount? I want to compare reads from 6 different samples.
Forum: Bioinformatics 02-02-2014, 01:44 AM
Replies: 10
Views: 3,942
Posted By roll
My understanding is that if i do the above, i...

My understanding is that if i do the above, i will get the miRNA count per gene. Whereas i am interested in is counting each miRNA type in each sample, like the table above. Is it possible to do that...
Forum: Bioinformatics 01-31-2014, 09:04 AM
Replies: 10
Views: 3,942
Posted By roll
What I am mising to understand is that my boss...

What I am mising to understand is that my boss wants to have a table like the following - for each mirna
Cond1 Cond2 Cond3
mirna1 3 5 7
mirna2 2 0 6


When I download the...
Forum: Bioinformatics 01-31-2014, 01:08 AM
Replies: 2
Views: 1,487
Posted By roll
How to check quality of SNPs

After running my SNP calling, what are the things i can check to see that my results are good quality? And i didnt do any sislly mistakes?
Forum: Bioinformatics 01-30-2014, 06:47 AM
Replies: 10
Views: 3,942
Posted By roll
mouse mm9 miRNA in gtf format

Hi,
Where can i find mouse miRNA mm9 reference data in gtf format?
I know mirbase but i could only found these in gff format.
I would like to use this for htseq-count.
Forum: Bioinformatics 01-30-2014, 01:54 AM
Replies: 3
Views: 2,155
Posted By roll
yes, they are all mapped properly. How can i...

yes, they are all mapped properly. How can i check if there is any other mistakes in the data?
Forum: Bioinformatics 01-29-2014, 07:34 AM
Replies: 3
Views: 2,155
Posted By roll
htseq-count error message

I keep getting the following error message when i use the htseq-count

Error occured when processing SAM input (line 9786565):
'pair_alignments' needs a sequence of paired-end alignments
...
Forum: Bioinformatics 11-13-2013, 03:52 PM
Replies: 3
Views: 1,504
Posted By roll
Thanks, i was looking at this feature. It is fast...

Thanks, i was looking at this feature. It is fast but i also want to know the repeat elements that are within certain threshold, 500bp for example in the forward strand.
This seems to be possible...
Forum: Bioinformatics 11-12-2013, 07:00 AM
Replies: 3
Views: 1,504
Posted By roll
how to summarize information for a gene from bam file

I have very basic question about bam files, it may be very obvious but kind of stacked.

I would like to see how many LINE,SINE etc are around the genes (which of my genes are enriched with repeats...
Forum: Bioinformatics 11-12-2013, 02:55 AM
Replies: 3
Views: 8,457
Posted By roll
what exactly does samtools view -x or -X do?

what exactly does samtools view -x or -X do?
Forum: Bioinformatics 11-12-2013, 02:15 AM
Replies: 24
Views: 6,014
Posted By roll
from the repeat list, i am trying to use the ones...

from the repeat list, i am trying to use the ones on forward strand. do you know how to extract this from the .out file?
The column headers are like
SW perc perc perc query position in...
Forum: Bioinformatics 10-17-2013, 02:13 AM
Replies: 2
Views: 2,756
Posted By roll
Thanks. I start using this and now it complaints...

Thanks. I start using this and now it complaints about libraries.

No search libraries were configured at /Downloads/fastq_screen_v0.4.2/fastq_screen line 119.

I assume it refers to the...
Forum: Bioinformatics 10-16-2013, 06:42 AM
Replies: 2
Views: 2,756
Posted By roll
how to detect contamination or sample preparation artifacts in sequencing results

Hi,

Is there any tool (apart from fastQC) to detect all primers/adapters(contaminants basically) in my raw fastq file that needs to be removed before mapping?
Forum: Bioinformatics 10-03-2013, 04:16 AM
Replies: 24
Views: 6,014
Posted By roll
I did the check. As you suggested the order is...

I did the check.
As you suggested the order is different.

The only differences are that
i have chrM in fa file and MN in the gtf file.
Also in the gtf file i have lots of 'NT_123456' type of...
Forum: Bioinformatics 10-02-2013, 06:34 AM
Replies: 24
Views: 6,014
Posted By roll
Do you mean manually checking if all chromosomes...

Do you mean manually checking if all chromosomes are there? i do not know what contigs are or how to check them.

I think chrX and Y are missing in the gtf file. But how can I find information for...
Forum: Bioinformatics 10-02-2013, 05:50 AM
Replies: 24
Views: 6,014
Posted By roll
I am using mm9. And I downloaded the bowtie index...

I am using mm9. And I downloaded the bowtie index from their webpage. I had to change the chr names as ensembl uses the 1 instead of chr1. But i don't know whether just adding chr in front of the...
Forum: Bioinformatics 10-02-2013, 05:32 AM
Replies: 24
Views: 6,014
Posted By roll
Thanks Devon, Very helpful so far. I...

Thanks Devon,
Very helpful so far.
I downloaded this annotation from ensembl. From biomart i simply left the filters sections empty and used the whole output as my list. This is right, no?

PS. i...
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