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Forum: Bioinformatics 07-16-2012, 11:55 PM
Replies: 1
Views: 880
Posted By droog_22
Bowtie mapping with distance to next best hit


I am using bowtie 0.12.7 to map 50mer paired-end Illumina reads to the hg19 assembly. With this command: bowtie -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa ...
Forum: Bioinformatics 02-09-2012, 08:53 AM
Replies: 0
Views: 1,642
Posted By droog_22
Simulating paired-end reads and bowtie alignments


I am simulating paired-end read data by extracting 36-mers from the dm3 genome and generating pairs of reads which are 550 bp apart. I then use bowtie to map the paired-end data like this:...
Forum: RNA Sequencing 02-02-2012, 10:00 PM
Replies: 2
Views: 2,196
Posted By droog_22
Update IGV


I once had many mismatches in another dataset which I aligned with novoalign. It was only later that I found out that novoalign introduces soft-clipped bases which my installed version of IGV...
Forum: Bioinformatics 01-09-2012, 08:09 AM
Replies: 0
Views: 1,117
Posted By droog_22
Finding regions of enriched sequence tags

Dear NGS community,

I am looking for an existing software package or library that would allow me to easily find regions in the dm3 genome which are enriched and cluster.

My data consists of...
Forum: Bioinformatics 01-06-2012, 11:54 AM
Replies: 2
Views: 2,056
Posted By droog_22
Hi Eric, You could use the some kind of user...

Hi Eric,

You could use the some kind of user tag, e.g. YC:Z:247,251,255 in our BAM file. You can later tell the UCSC genome browser (or IGV) not to color the BAM track by the strand of the read...
Forum: Bioinformatics 11-04-2011, 08:01 AM
Replies: 1
Views: 2,275
Posted By droog_22
Re-write strand information in BAM file


I have a quick and simple questions: Is there a ready-to-use tool which allows me to re-write the strand information in a BAM file, such that reads which mapped on the forward strand are...
Forum: Bioinformatics 04-04-2011, 08:26 AM
Replies: 514
Views: 223,062
Posted By droog_22
Counting Hits in a BAM file

Dear All,

I am using bowtie to align reads to the dm3 genome. I just read that the SAM specifications allow for tags such as H0, H1, etc. which counts the number of 0-differences, 1-difference...
Forum: Bioinformatics 02-11-2011, 12:32 AM
Replies: 7
Views: 11,442
Posted By droog_22
Hi, You can use genomeCoverageBed from the...


You can use genomeCoverageBed from the which can also read in BAM files.

Forum: Bioinformatics 02-02-2011, 11:55 PM
Replies: 1
Views: 3,510
Posted By droog_22
Hi, It seems that the problem might be due...


It seems that the problem might be due to some illegale or out of range phred scores as the error message says "Cannot encode phred score: 253". You might want to have a look here...
Forum: Bioinformatics 01-17-2011, 02:31 AM
Replies: 4
Views: 11,189
Posted By droog_22
BAM files can contain mapped and unmapped reads

Dear Azazel,

Using samtools view you are counting the complete number of reads in your BAM file - be it mapped or unmapped reads.

$ samtools view data.bam | wc -l

Information about which...
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