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Significant variation in FastQ File Sizes - Fragmentation Issue?
Hi all, I’m pretty new to NGS and library prep. I just completed library prep and WES for a pilot of 12 FFPE DNA samples, and got back Fastq files that... -
Fragment length for expression estimation
I have sequenced using Illumina and quantified with Salmon. I have run some QC plots and have what looks like a spurious sample (see attached)
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bowtie2 fragment length
Dear Bowtie2 user,
I have a question regarding the fragment length issue.
The reads that mapped to the different chromosomes... -
150bp-1.3kb insert size PE on HiSeq
I have a library that I am running on a HiSeq2000 for PE-100 reads. The fragment sizes range from 150bp to 1.3kb. I can't do much about this range since... -
Variable length paired-end read processing using Cufflinks
Hi All,
My RNA-seq data has low qualities in the tail. So I trimmed the reads which leads to my reads with variable length. TopHat support... -
TruSeq RNA initial concentration and Ampure beads
Greetings!
I am getting ready to use the TruSeq RNA kit for the first time. I noticed the concentration of Ampure beads to sample decreases... -
Cufflinks calls incorrect read length
I am working with RNA-Seq 36 bp single-end reads (unstranded) from several experimental conditions, which have been aligned to my reference genome using... -
Fragment length Illumina
1. Is there an upper size limit of fragment binding to the Illumina flow cells?
2. Would this be the same for Illumina GSII and for HS2000?... -
Cufflinks' estimated fragment length mean and standard deviation
I have a question about the Fragment Length Distribution that Cufflinks (v 0.9.0+) estimates, based on paired end read alignments:
Is...
