User: landrjos

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landrjos0
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Posts by landrjos

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Help with DeepTools
... Hi All, A reviewer of our paper wants us to show the input normalized read density for our ChIP-Seq data in the IGV browser shots we have in several of our figures. I would like to use bamCompare from deepTools to do this input normalization and output as a BW file which can be viewed in IGV. I ca ...
software error deeptools chip-seq written 7 weeks ago by landrjos0 • updated 7 weeks ago by genomax42k
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Illumina Adapter in R1 Only
... Hi All, I notice in my FastQC results from several paired end Illumina sequencing runs that the adapter-index primer is an overrepresented sequence in the R1 fastq file only, and not in the R2 fastq file. Is that because the FastQC is searching with the complement Adapter sequence which would be th ...
sequence sequencing written 3 months ago by landrjos0 • updated 3 months ago by chen1.5k
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Comment: C: Help with Fastq-Tools Install
... Hi, I'm the I.T. analyst working to help get this installed. What should we be logged in as exactly? You stated we cannot install globally, but I'm the admin on this machine. By globally, what exactly do you mean? Are you saying we need superuser privileges? ...
written 3 months ago by landrjos0
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Comment: C: Help with Fastq-Tools Install
... The problem we are having is that the fasts-tools does not come with a readme file. There are no install instructions at all. Would the install path be in the program folder /Users/jwlandry2/Desktop/Bioinfor.Tools/fastq-tools-0.8? here are the contents of the fastq-tools folder. AUTHORS TODO co ...
written 3 months ago by landrjos0
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Comment: C: Help with Fastq-Tools Install
... This is a university computer. What do I need the IT people to do? ...
written 3 months ago by landrjos0
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Help with Fastq-Tools Install
... Hi All, I am trying to install fasts-tools. I have successfully installed pcre2 and libc but cant install fasts-tools build 8. This is the error I am getting. Can anyone give a suggestion as to what I am doing wrong? Making install in src CC common.o CCLD fastq-grep ...
software error next-gen sequencing written 3 months ago by landrjos0 • updated 3 months ago by Kevin Blighe12k
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Comment: C: How to tell if a FastQ file is a concatinate of 2 seperate illumina runs?
... I think with both the flow cell and barcode information from the fast q files I can figure it out. Thanks for your help. ...
written 3 months ago by landrjos0
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Comment: C: @RG information from Bowtie2 Alignments
... I am not a professional. Could you suggest some changes to the script to retain the read group information? ...
written 3 months ago by landrjos0
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Comment: A: @RG information from Bowtie2 Alignments
... Here is the script I am using to run Bowtie2....Where would I add the read group information? #!/bin/bash #shell #$ -S /bin/bash #$ -pe smp_2 10 ##### export OMPI_MCA_orte_rsh_agent="rsh:ssh" ##### export LD_LIBRARY_PATH=/usr/global/openmpi-1.5.3-w-psm/lib:$LD_LIBRARY_PATH ...
written 3 months ago by landrjos0 • updated 3 months ago by Devon Ryan76k
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@RG information from Bowtie2 Alignments
... Hi All, I use Bowtie2 to align my Illumina Fastq sequence files then convert to BAM using Samtools. The BAM output file does not have any barcode information. Or any @RG information at all. Here is the header from one of the BAM files.... Does Bowtie2 save this information? If so I would I acce ...
next-gen alignment chip-seq sequencing written 3 months ago by landrjos0 • updated 7 weeks ago by Biostar ♦♦ 20

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