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Comment: How to remove Illumina TruSeq Index adapters reverse (R2 reads )
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GenoMax
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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…
Comment: Genozip: A new compression tool for FASTQ, BAM, VCF and more
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matthew.pobox
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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…
Comment: get read length from sra
by
Renesh
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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…
Comment: Primers trimming from Illumina paired-end reads by BBDuk software
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GenoMax
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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…
Answer: Database for Enhancers with Coordinates
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Papyrus
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Also check [EnhancerAtlas][1], apart from coordinates it provides predictions for enhancer-gene target interactions, which may be useful.
…
Comment: get read length from sra
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GenoMax
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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…
Comment: Interpreting output of BCFtools RoH
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gubrins
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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.
Comment: rsem-calculate-expression with STAR takes forever but without error
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Fleur
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Thanks both! I will try :) :)
Comment: rsem-calculate-expression with STAR takes forever but without error
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Fleur
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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…
Comment: which tool can I use to detect CNVs?
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patelk26
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You could try CNVkit. You can create a reference copy number profile without normal samples.
Answer: Is there any software that can use ATAC-seq to identify super enhancer
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jared.andrews07
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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 …
Comment: script to organize files
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Galileo
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I found a solution: used dos2unix on the files that have '$'\r' at the end :)
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