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anthill_sri017 [2021/01/21 16:38] – created 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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   mkdir -p /home/users/${USER}/anthill23_preseq/preseq-3.1.2   mkdir -p /home/users/${USER}/anthill23_preseq/preseq-3.1.2
   ../configure --prefix="/home/users/${USER}/anthill23_preseq/preseq-3.1.2" --enable-hts   ../configure --prefix="/home/users/${USER}/anthill23_preseq/preseq-3.1.2" --enable-hts
 +  
   make -j${SLURM_NPROCS} && make install    make -j${SLURM_NPROCS} && make install 
      
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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 ''090413_I352_FC31307AAXX_L6_SORssqRADDHAAPE_1.fq.gz'' and run it with AdapterRemoval software. This job will take about 10 minutes, inspect job output ex.: ''slurm-1949.out'' for AdapterRemoval 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 ''adapterremoval_test.batch'' :+File ''preseq_test.sbatch'' :
  
 <code> <code>
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 #SBATCH --ntasks=2 #SBATCH --ntasks=2
 #SBATCH --mem 4G #SBATCH --mem 4G
-#SBATCH --job-name AdapterRemoval_test+#SBATCH --job-name preseq_test
  
 #prepare temporary folder #prepare temporary folder
 cd `mktemp -d -p ~/` cd `mktemp -d -p ~/`
  
-#download fq file +#download bam filefq file 
-wget wget ftp://download.big.ac.cn/SorghumVB/fastq/090413_I352_FC31307AAXX_L6_SORssqRADDHAAPE_1.fq.gz+wget --no-check-certificate http://hgdownload-test.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1.bam
  
-#export path to AdapterRemoval binary+#export path to preseq-3.1.2 binary
 export PATH=$PATH:/home/users/${USER}/anthill23_preseq/preseq-3.1.2/bin export PATH=$PATH:/home/users/${USER}/anthill23_preseq/preseq-3.1.2/bin
  
-#use AdapterRemoval software +#predict the yield of a future experiment if the input file is in .bam format 
-AdapterRemoval --file1 090413_I352_FC31307AAXX_L6_SORssqRADDHAAPE_1.fq.gz --qualitybase 64 +preseq lc_extrap -B -o yield_estimates.txt wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1.bam
  
 </code> </code>

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