Hi,
I am working on rna-seq data analysis..
Mapped the reads to transcriptome reference (cDNA fasta file) for wheat using Bowtie2....
10 results in 0.0029 seconds.
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How to get read-counts for sam files with transcriptome reference??
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Bowtie preference for earlier alignments?
So, I aligned my small RNA reads using the following command in bowtie.
bowtie -S -a -v 1 -m 1 --best --strata Reference/Release4.3/dmel_rel4_3... -
Small RNA Read Counts
New to NGS data, currently analyzing small RNA seq data with emphasis on piRNAs, looking to eventually do differential expression analysis. I have my...Last edited by WHP; 04-28-2014, 11:53 AM. -
Sicer questions
I am using Sicer to examine data from DNMT1 binding by ChIP-seq. I run IP and input and want to know
1) what is the ChIP island Read Count and... -
Samtools view -c Readcount Issue
I'm using samtools to determine the total number of reads in a uniquely large bam file as shown below. I'm having a hard time interpreting the result.... -
read counts without gff3 file
I am working with a species that does not have a genome sequenced. There is a partial unigene/EST database that I have used to align some Illumina RNA-Seq... -
Issue with htseq-count
Hello,
I am working on an RNA-Seq project in soybean. I used Illumina HiSeq for single end reads on my soybean samples and am working on my alignment.... -
Cuffdiff and zero FPKM values give enormous log ratio
Hi all,
I'm new to RNA seq and I'm working with TopHat - Cufflinks - Cuffcompare - Cuffdiff pipeline.
I use Cufflinks without annotation... -
Using DESeq to examine control variability
Dear all,
I have count data for 2 conditions, 10 normal samples (N) vs 10 diseased samples (D). When I compare for differential expression... -
Number of Reads in 454 Library
What's the average/range of the total number of reads in 454 library?
