22 results in 0.0029 seconds.
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How to get better alignment results of PAcBio data?
HI. I am trying to align PAcBio data (data from third generation sequencer) using bwa mem. I am getting very less number of aligned reads in SAM file... -
Paired end SAM to single end
I am performing PAR-CLIP which is typically done using single end however we ran paired because it fit in with our in house set up.
I've... -
Sam file from alignment of Solid Colorspace reads using Bowtie
Hi everyone, I am mapping color-space fasta and QV files (sequenced in ABI SOLID) from a human exome, using the reference given by the GATK resources... -
Help with sorting sam files in python!
Hello All!
I am new to coding. I have written a python script to analyze a bunch of fastq files from RNASeq analysis. I am using the subprocess... -
Probelem with SAM file created by Bowtie2
Hello everyone,
I created a bowtie index from a fasta file which was merged from 4 individual fasta file. One is from miRBase, two from RFAM...Last edited by newfie; 09-21-2016, 09:25 AM. Reason: one output file name was not mentioned correctly -
Difference between sequence coverage and physical coverage
Hi to everyone,
I'm looking to understand the difference between these two kinds of coverage:
Sequence Coverage and Physical... -
Sequence Coverage and Genome Insertion lenght from SAM
Hi to everyone,
I'm quite new of this science, and I'm looking for solve a problem.
I've a SAM file generated by BWA and... -
Is SAMtools the right software for this project?
Hi Everyone,
Here is a brief summary of what I am trying to do with my project: Essentially, I want to find how a mutation in the mRNA... -
views Bowtie2 : aligned result read count not matching with sam Read count
bowtie2 -f -N 1 -p 8 -x REF.fa -1 sample01_1.fasta -2 sample01_2.fasta -S sample01.sam --al sample01_al.fasta --al-conc sample01_alcon.fasta
...Last edited by vinumanikandan; 05-13-2015, 03:05 AM. -
Editing genome assemblies with Cytoscape
Hi All,
I have performed a metagenomic assembly from Ion-Proton reads. Now I want to check my assembly using Cytoscape for probable misassembles.... -
Specifying read group info for multiple samples per lane in SAM/BAM files (for GATK)
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Zero counts in htseq-count output
I am pretty desperate, so if anyone has any advice, I will be forever grateful.
Basically, I am using the following command:
... -
Online tools to generate count tables from sam/bam files
Does Galaxy or any other online tools offer methods to generate a count table from bam or sam files? -
SAM files aligned by Bowtie - Mystified.
Hi,
This is one of my first forays in SOLID data so please bear with me if the question is basic;
I had aligned SOLID data... -
Can you tell recombination/conversion from SAM flags?
Hi all,
I have tried for some time now to figure out if I can detect recombination or gene conversion using discordantly mapping reads...
