2020+ Posts

C: Varying assembly statistics: Abyss & SPades by h.mon ♦ 26k
I suspect 1000x is too high coverage, you should reduce it with digital normalization or just pla...
C: awk extract certain line by mxlsherry1992 • 30
Hi all, it all worked, Thank you and have a great day!!
C: Varying assembly statistics: Abyss & SPades by max_19 • 110
That is good to know, thank you! Expected assembly size is ~4.8MB. Adapters have been trimmed and...
C: Interpreting Hisat2 alignment output by ATpoint ♦ 21k
Model organism? What is the read length, is the reference genome of high quality and is this any ...
C: Chip-seq H3k27 Bowtie2 Alignement by ATpoint ♦ 21k
Agreed. Once you filter for a mapping quality that is not basically zero (I always do 20) they're...
A: Varying assembly statistics: Abyss & SPades by h.mon ♦ 26k
If you look at the total assembly size of contigs greater than 50k, you will see you have approxi...
C: Chip-seq H3k27 Bowtie2 Alignement by colin.kern • 320
Very standard practice to remove multi-mapped reads in ChIP-seq analysis. The ENCODE and Roadmap ...
C: Chip-seq H3k27 Bowtie2 Alignement by zeeshan.fazal1986 • 0
sorry. Its H3K27me3.
C: Chip-seq H3k27 Bowtie2 Alignement by colin.kern • 320
H3K27 is not a mark, H3K27me3 and H3K27ac are marks, and have very different properties. So you s...
A: What does the final RNA-Seq library for sequencing by Illumina contain? ss cDNA by ATpoint ♦ 21k
The library itself is double stranded as standard PCR **always** produces dsDNA. The library is d...
C: Chip-seq H3k27 Bowtie2 Alignement by ATpoint ♦ 21k
Yes, manually blasting some random reads might give you an idea if contamination is the source of...
C: Chip-seq H3k27 Bowtie2 Alignement by zeeshan.fazal1986 • 0
how can I achieve this? I never did this? I have aligned .sam files. Should I get unaligned reads...

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