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Forum: Bioinformatics 09-06-2017, 06:56 AM
Replies: 1
Views: 789
Posted By heso
How to pile up reads and get per base coverage?

Hi,

I have list of sequences (17-35bases) with sequence read count in column 1.
I would like to see the end processing patterns of these sequences (to pile up similar ones and get the per-base...
Forum: Bioinformatics 03-22-2017, 01:41 AM
Replies: 0
Views: 825
Posted By heso
Collapsing gene names based on partial string overlap

I have a long list of gene names with corresponding read counts. I'm mainly interested that the tRNAs with an identical anticodon are collapsed and the sum of their read counts is calculated.
...
Forum: Bioinformatics 12-08-2016, 07:14 AM
Replies: 1
Views: 1,561
Posted By heso
Listing which biotypes are present in an Ensembl .gtf file

I'm trying to find out which gene_biotypes are described in the Human gtf file from Ensembl.
The head of the file looks like that:

1 havana gene 19072110 19075511 . ...
Forum: Bioinformatics 05-18-2016, 06:38 AM
Replies: 2
Views: 1,704
Posted By heso
Thanks Michael, it worked perfectly!! /Helena

Thanks Michael, it worked perfectly!!

/Helena
Forum: Bioinformatics 05-18-2016, 02:12 AM
Replies: 2
Views: 1,704
Posted By heso
Can I use htseq --samout file for subsequent annotation?

Hi,
So briefly what I'm doing is that:
-->I'm annotating my smallRNA sequencing data using htseq-count.
-->I'm using original.sam to annotate miRNAs and using -o to get the out.sam
-->From that...
Forum: Illumina/Solexa 12-17-2015, 03:44 AM
Replies: 2
Views: 1,853
Posted By heso
Thanks a lot. MultiQC had the features I was...

Thanks a lot. MultiQC had the features I was looking for.
Forum: Illumina/Solexa 12-14-2015, 04:57 AM
Replies: 2
Views: 1,853
Posted By heso
combining multiple fastqc output files

Hi,

I'm trying to combine several FastQC results files to create one overview file.

I found a script for this as well, but have no idea how to access that:...
Forum: Bioinformatics 12-10-2014, 06:02 AM
Replies: 0
Views: 1,316
Posted By heso
Question DESeq data transformation and creating a heatmap

Hi,

I have a question about varianceStabilizingTransformation and creating heatmaps.

The data is without biological replicates, therefore:
cds0_trial=estimateDispersions(cds0_trial,...
Forum: Bioinformatics 11-17-2014, 12:57 AM
Replies: 3
Views: 11,826
Posted By heso
I got it fixed now. I used this site for...

I got it fixed now. I used this site for downloading.
ftp://ussd-ftp.illumina.com/Mus_musculus/UCSC/mm10/

There I found the gtf in the format I wanted.
Thanks everybody:)
Forum: Bioinformatics 11-16-2014, 03:14 AM
Replies: 3
Views: 11,826
Posted By heso
Question UCSC mm10 gtf file

Hi,
I have dowloaded UCSC hg19 gtf files from Galaxy
...
Forum: Bioinformatics 11-14-2014, 12:14 PM
Replies: 8
Views: 4,213
Posted By heso
Yes, that's what it seemed to be. I downloaded...

Yes, that's what it seemed to be.
I downloaded ebwt as well as gtf files from the UCSC site and now everything worked :)



Thanks again to everybody for helping out !
Forum: Bioinformatics 11-13-2014, 10:58 PM
Replies: 8
Views: 4,213
Posted By heso
The .summary file contents is the following: ...

The .summary file contents is the following:

Status Rd4_UCexo_r1_seqok_n0l15abest_hg37_onlymapped.bam
Assigned 0
Unassigned_Ambiguity 0
Unassigned_MultiMapping 0...
Forum: Bioinformatics 11-13-2014, 12:06 PM
Replies: 8
Views: 4,213
Posted By heso
hi again, I tried You suggestion. Still no...

hi again,

I tried You suggestion. Still no help:(


//================================= Running ==================================\\
|| ...
Forum: Bioinformatics 11-13-2014, 07:16 AM
Replies: 8
Views: 4,213
Posted By heso
Thank you for the answere. I now tried the...

Thank you for the answere.
I now tried the following command:



of some reason I still get 0% successfully assigned reads:


The output file looks like that:
Forum: Bioinformatics 11-13-2014, 05:41 AM
Replies: 8
Views: 4,213
Posted By heso
Question featureCounts error

Hi,

I have a problem with featureCounts gtf file.

I want to count the miRNA reads using the sorted .bam file containing only mapped reads (all generated by samtools from Bowtie output --SAM...
Forum: Bioinformatics 11-08-2014, 09:19 AM
Replies: 1
Views: 1,240
Posted By heso
different results in samtools flagstat and bowtie

Hi,

I'm mapping human single-end miRNA reads to the genome using bowtie -v0 -k5
The reads are in fasta format and collapsed with fastX_collapser

So, for a stats output from bowtie I get:
#...
Forum: Bioinformatics 10-31-2014, 04:00 AM
Replies: 4
Views: 1,678
Posted By heso
Thank you for all the answers. I tried out awk...

Thank you for all the answers.
I tried out awk and it worked perfectly. Thanks again, I could not have figured it out myself :)
Forum: Bioinformatics 10-30-2014, 06:11 AM
Replies: 4
Views: 1,678
Posted By heso
reformatting a FASTA file

Hi,
I need to process my miRNA fasta file to end up with a collapsed fasta (read count format).
I have used fastx_collapser for this task, that gives me the following output:

>1-327278...
Forum: Bioinformatics 09-29-2014, 04:28 AM
Replies: 1
Views: 1,500
Posted By heso
Question how to extract miRNA spike-in controls from smallRNAseq data

Hi,
I'm processing single end Illumina Hiseq2000 miRNA data. I've got 5 miRNA spike-in controls in my samples. How could I extract those from the rest of my data? I would like to end up with 2...
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