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Can you post an example of what you are referring to? Normally trimming programs should check reverse complements of sequences they are loo…
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This seems like a great tool which has been seriously overlooked.
I've been testing it out and was able to reproduce the compression ra…
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The suggested methods works. Here is another method using the [SRA toolkit][1]
fastq-dump -X 1 -Z SRR5790106 | sed -n '2p' | awk '{ pr…
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Following should work. Give it a try and let me know.
bbduk.sh -Xmx2g in1=test_R1.fq in2=test_R2.fq out1=R1_trim.fq out2=R2_trim.fq li…
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Also check [EnhancerAtlas][1], apart from coordinates it provides predictions for enhancer-gene target interactions, which may be useful.
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You will only get average length of reads (which may or may not be very useful) using [Entrezdirect][1].
$ esearch -db sra -query "SRR…
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Heys, did you manage in interpreting and visualizing the output? I'm in the same situation...
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`cnvkit` and `ExomeDepth` are great tools for that. Also, both are pretty straightforward to use.
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Thanks both! I will try :) :)
Comment: rsem-calculate-expression with STAR takes forever but without error
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Ah yes, sounds similar to tmux which is what I'm using. That also makes sure that the job keeps running when you close the terminal. Thanks…
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You could try CNVkit. You can create a reference copy number profile without normal samples.
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The original paper actually used a collection of TFs + Mediator. ROSE was not designed for H3K27ac use, though both the authors and others …
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I found a solution: used dos2unix on the files that have '$'\r' at the end :)
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