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anthill_sri017 [2021/01/21 16:55] – tmatejukanthill_sri017 [2023/08/01 01:08] (current) – external edit 127.0.0.1
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 ==== description ==== ==== description ====
-AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. Software page : [[https://github.com/MikkelSchubert/adapterremoval]], software usage examples [[https://adapterremoval.readthedocs.io/en/latest/examples.html]] .+The preseq package is aimed at predicting the yield of distinct reads from a genomic library from an initial sequencing experiment. Software page : [[https://github.com/smithlabcode/preseq]].
  
 ==== software version ==== ==== software version ====
-Bellow description covers AdapterRemoval version 2.3.1 .+Bellow description covers preseq version 2.3.1 .
  
 ==== prepare software ==== ==== prepare software ====
-Login to anthill23, start interactive session in which download and compile AdapterRemoval ((this will take 3 minutes)):+Login to anthill23, start interactive session in which download and compile preseq ((this will take 3 minutes)):
  
   @anthill23:~$ srun -n 2 --mem=4G --pty bash -l   @anthill23:~$ srun -n 2 --mem=4G --pty bash -l
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 ==== sbatch example ==== ==== sbatch example ====
 This description assumes that above step ( prepare software ) were done beforehand. \\ This description assumes that above step ( prepare software ) were done beforehand. \\
-Bellow slurm job creates temporary folder in your home folder (like ''tmp.AtrQrrJi3W''), then downloads file ''wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1.bam'' and run preseq on it. This job will take about 10 minutes, inspect job output ex.: ''slurm-1949.out'' for preseq output messages.+Bellow slurm job creates temporary folder in your home folder (like ''tmp.AtrQrrJi3W''), then downloads file ''wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1.bam'' and run preseq on it ((this will take 2 minutes)). \\ 
 +Inspect job output ex.: ''slurm-1949.out'' and ''yield_estimates.txt'' file for preseq output messages and output.
  
 File ''preseq_test.sbatch'' : File ''preseq_test.sbatch'' :
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 #download bam filefq file #download bam filefq file
-wget http://hgdownload-test.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1.bam+wget --no-check-certificate http://hgdownload-test.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1.bam
  
 #export path to preseq-3.1.2 binary #export path to preseq-3.1.2 binary

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