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Forum: Bioinformatics 05-11-2015, 09:12 AM
Replies: 0
Views: 1,249
Posted By skingan
peak identification with macs2 for small RNA data

Hello,

I have illumina data from small RNAs and am using MACS2 to identify peaks in read mapping. (Read mapping done with bowtie1.) This method was developed for ChIP-Seq so I need to tweak the...
Forum: RNA Sequencing 05-07-2015, 08:32 AM
Replies: 5
Views: 1,392
Posted By skingan
Okay, I see it now. Thanks!

Okay, I see it now. Thanks!
Forum: RNA Sequencing 05-07-2015, 08:26 AM
Replies: 5
Views: 1,392
Posted By skingan
Thanks for your reply, dpryan. But if I have a...

Thanks for your reply, dpryan. But if I have a non-zero edit distance, shouldn't there be some X's in the cigar? Here are some fields from my file:

MapQ: 255
CIGAR: 30M
NM:i:2

And an...
Forum: RNA Sequencing 05-07-2015, 07:58 AM
Replies: 5
Views: 1,392
Posted By skingan
This thread answers the mapQ question: ...

This thread answers the mapQ question:

http://seqanswers.com/forums/showthread.php?t=7815

But I'm still confused about the cigar.
Forum: RNA Sequencing 05-07-2015, 06:38 AM
Replies: 5
Views: 1,392
Posted By skingan
bowtie CIGAR and MapQ errors

Hello,

I am mapping illumina reads of small RNAs to the Drosophila genome using bowtie1. My command:

bowtie -S -n 0 -l 15 -k 200 --best ref.fa reads.fq > file.sam

The map qualities and...
Forum: Bioinformatics 02-26-2014, 11:05 AM
Replies: 1
Views: 1,657
Posted By skingan
tophat/bowtie compatibility

Hi nerds,
I am using the Tuxedo suite for an RNAseq dataset. Apparently the latest versions of bowtie2 and tophat are incompatible. Does anyone know what versions of the programs play nice?
Thank...
Forum: Bioinformatics 12-04-2013, 11:42 AM
Replies: 1
Views: 3,764
Posted By skingan
Angry bam -> vcf -> fasta

Hi Everyone,

I am trying to generate a FASTA sequence from a BAM file using a BCF/VCF file as an intermediate. I would like to create a temporary BCF/VCF file from which I can make a FASTA...
Forum: Genomic Resequencing 05-08-2013, 09:14 AM
Replies: 0
Views: 3,801
Posted By skingan
XA tag from bwa

Hi everyone,

I am mapping 36bp Illumina reads to a reference genome using BWA. When I convert my SAM output to BAM format with SAMTOOLS VIEW I get the following stderr:

[samopen] SAM header is...
Forum: De novo discovery 05-02-2011, 08:35 AM
Replies: 8
Views: 5,140
Posted By skingan
Hi Thorondor, The % identity should be very...

Hi Thorondor,
The % identity should be very high, <3% divergence for the orthologous sequences. The problem is that there are many repeat elements in and around the genes so the structure is not...
Forum: De novo discovery 04-29-2011, 07:11 AM
Replies: 8
Views: 5,140
Posted By skingan
Targeted de novo assembly

Hello,

I have an interesting problem I am looking for some advice.

I have whole genome resequence PE illumina data and I am interested in doing a de novo assembly of three particular genes....
Forum: De novo discovery 08-10-2010, 07:17 AM
Replies: 0
Views: 2,050
Posted By skingan
mira quality scores

Hi,
Does anyone know what scale mira uses for the quality scores of the assembly? I have generated project_out.padded.fasta and project_out.padded.fasta.qual files; does the qual file contain Sanger...
Forum: Genomic Resequencing 07-29-2010, 01:02 PM
Replies: 0
Views: 2,522
Posted By skingan
IMAGE input files

Hi,

We are using IMAGE to fill in gaps of our genome assembly but are not sure how to generate the required input files:

contigs.fa.original and
read.placed.original...
Forum: Genomic Resequencing 07-22-2010, 06:50 AM
Replies: 21
Views: 16,682
Posted By skingan
It turned out to be a similar problem to the one...

It turned out to be a similar problem to the one SMHfrog had. In my reference file, each chromosome sequence was on a single line, so when samtools built the .fai file there was a segmentation fault...
Forum: Genomic Resequencing 06-16-2010, 02:06 PM
Replies: 21
Views: 16,682
Posted By skingan
No. All of the positions in the pileup file are...

No. All of the positions in the pileup file are N's and my reference sequences do not consist of all N's.
Sarah
Forum: Genomic Resequencing 06-16-2010, 01:59 PM
Replies: 21
Views: 16,682
Posted By skingan
my command: samtools pileup -f myref.fas...

my command:

samtools pileup -f myref.fas my_sorted_assembly.bam -c > mydata.pileup

my output (e.g.):

NT_033777 27895205 N A 24 0 6 17 aaaaaaaaaaaaaaaaa $))))))()')))")))
Forum: Genomic Resequencing 06-14-2010, 11:05 AM
Replies: 21
Views: 16,682
Posted By skingan
samtools problems with reference in pileup file

Hello,

I am using samtools to generate a pileup file from a Mosaik genome assembly. My problem is that the pileup file contains all "N's" in the reference sequence field (column 3). I have double...
Forum: Bioinformatics 06-07-2010, 09:32 AM
Replies: 7
Views: 2,586
Posted By skingan
I'm having this problem too. I am working with...

I'm having this problem too. I am working with both a 454 dataset and a solexa dataset. I am running each of the chromosomes separately and I can get gigaBayes to work for all but 1 of the...
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