User: gdeniz

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gdeniz0
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Posts by gdeniz

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How to quantify mutations by type (e.g. A>T, T>A, G>C, ...) within reads mapping to genes
... Hi, I have RNA-seq data and would like to quantify the number of mutations and their type in reads mapping to genes probably normalized by gene size. Is there a simple solution for this or a package you would recommend? Thanks for your pointers! ...
rna-seq written 5 days ago by gdeniz0
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Comment: C: MACS2: Albeit outdir definition, my output goes to folder of input
... That echo call made me realize what is wrong: the `$infile` variable seems to overwrite the output dir because it contains an absolute path. Changing the call option to: --rfile $(basename ${infile%.sorted.dedup.bam}_model.r) solves the problem. Thanks for pointing me towards the answer! ...
written 9 months ago by gdeniz0
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Comment: C: MACS2: Albeit outdir definition, my output goes to folder of input
... Here is the echo'd output: macs2 predictd -i /mnt/iscsi_speed/blelloch/deniz/buecker2014/naive/bam/SRR1202453.sorted.dedup.bam -f BAM -g mm -m 5 50 --outdir "/mnt/iscsi_speed/macs2/qc" --rfile /mnt/iscsi_speed/bam/SRR1202453_model.r ...
written 9 months ago by gdeniz0
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Comment: C: MACS2: Albeit outdir definition, my output goes to folder of input
... I get the following error: /opt/sge625/sge/default/spool/go-node-38/job_scripts/114466: line 17: macs2 predictd -i ${infile} -f BAM -g mm -m 5 50 --outdir "${workdir}/macs2/qc" --rfile ${$infile%.sorted.dedup.bam}_model.r: bad substitution Here an attempt to clarify my parameters: workdir ...
written 9 months ago by gdeniz0
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Comment: C: MACS2: Albeit outdir definition, my output goes to folder of input
... Thanks for your suggestions, always happy to improve my quoting. Unfortunately, this didn't seem to solve the issue: INFO @ Tue, 04 Sep 2018 08:41:05: # Generate R script for model : /mnt/iscsi_speed/bam/SRR1202461_model.r Any other ideas? Do you think it is a quoting issue? ...
written 9 months ago by gdeniz0
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MACS2: Albeit outdir definition, my output goes to folder of input
... Hi, I seem to have a problem getting my output in the right location. Using the following call.. workdir="$1" files=($(awk '{print $1}' $2 )) infile="$workdir"/bam/${files[$SGE_TASK_ID]}.sorted.dedup.bam macs2 predictd -i $infile -f BAM -g mm -m 5 50 --outdir "$workdir"/macs2/qc -- ...
macs2 chip-seq written 9 months ago by gdeniz0

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