User: pt.taklifi

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pt.taklifi60
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Posts by pt.taklifi

<prev • 39 results • page 1 of 4 • next >
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samtools index error
... Hello everyone I am trying to extract uniquely aligned reads and sort them with `samtools` with the following command samtools view -h -f 2 -q 10 -bS -@ 20 hg38.sam | samtools sort -n -@ 1 > hg38.sort.bam after this when I try to index the output file samtools index hg38.sort.bam I ...
alignment written 3 days ago by pt.taklifi60 • updated 3 days ago by Pierre Lindenbaum134k
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5 follow
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how to select features for high dimension data?
... Hello everyone. I have a data set with dimension of 330 * 45000 ( 330 samples and 45000 features : reads in peaks) I am looking for a way to select best features for binary classification. so far I only chose feature with `covariance` higher than 0.5 or less than -0.5 and reduced dimension to 14000 ...
machine_learning high_dimension written 5 days ago by pt.taklifi60 • updated 4 days ago by Mensur Dlakic9.0k
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Comment: C: nohup with while loop
... this seems to work right now. Thank you! ...
written 19 days ago by pt.taklifi60
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Comment: C: nohup with while loop
... I installed the latest version of SRAtoolkit. I don't think with this version specifying file vdb-config -i works. here is what I [found][1] [1]: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=dbgap_use#s-3 ...
written 19 days ago by pt.taklifi60
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nohup with while loop
... Hi everyone. I am trying to download a list of sra files from SRA sever. I stored all SRA accession codes in a file named `accList.txt` so that each line is one accession code. I want to use `nohup` to download all of the files automatically . I run the code below but it seems that it does not wor ...
sratoolkit loop bash written 19 days ago by pt.taklifi60
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Comment: C: error with bowtie2 alignment
... thank you @ATpoint . as suggested , I think I should remove poor quality reads in trimming step. can I remove them with skewer ? ...
written 21 days ago by pt.taklifi60
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Comment: C: error with bowtie2 alignment
... I downloaded the fastq files from SRA . I will check if the problem is with fastq files. Thank you ...
written 21 days ago by pt.taklifi60
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Comment: C: error with bowtie2 alignment
... skewer -f sanger -m pe -x Nextera.fa read1.fastq read2.fastq ...
written 21 days ago by pt.taklifi60
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error with bowtie2 alignment
... Hi I am trying to align a fastq file to mitochondrial genome with bowtie 2 with the following command and store unmapped read to folder `unaligned` bowtie2 -p 1 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /home/ptaklifi/genome_folder/rCRSd/bowtie2_index/default/rCRSd --rg-id SRR10984460 -U SRR ...
alignment error sequencing written 21 days ago by pt.taklifi60
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Comment: C: bcftools variant calling
... you could use pipelines such as [varsan][1] or [strelka][2] [1]: http://varscan.sourceforge.net/germline-calling.html [2]: https://github.com/Illumina/strelka ...
written 25 days ago by pt.taklifi60

Latest awards to pt.taklifi

Supporter 21 days ago, voted at least 25 times.
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: how to get GC content of multiple ranges in R
Scholar 11 weeks ago, created an answer that has been accepted. For A: how to get GC content of multiple ranges in R

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