User: pt.taklifi
pt.taklifi • 60
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Posts by pt.taklifi
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2
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1
answer
67
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1
answer
... 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 ...
written 3 days ago by
pt.taklifi • 60
• updated
3 days ago by
Pierre Lindenbaum ♦ 134k
7
votes
1
answer
93
views
5 follow
1
answer
... 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 ...
written 5 days ago by
pt.taklifi • 60
• updated
4 days ago by
Mensur Dlakic • 9.0k
0
votes
1
answer
138
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1
answers
Comment:
C: nohup with while loop
... this seems to work right now. Thank you! ...
written 19 days ago by
pt.taklifi • 60
0
votes
1
answer
138
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1
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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.taklifi • 60
7
votes
1
answer
138
views
1
answer
... 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 ...
written 19 days ago by
pt.taklifi • 60
0
votes
0
answers
86
views
0
answers
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.taklifi • 60
0
votes
0
answers
86
views
0
answers
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.taklifi • 60
0
votes
0
answers
86
views
0
answers
Comment:
C: error with bowtie2 alignment
... skewer -f sanger -m pe -x Nextera.fa read1.fastq read2.fastq ...
written 21 days ago by
pt.taklifi • 60
2
votes
0
answers
86
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0
answers
... 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 ...
written 21 days ago by
pt.taklifi • 60
0
votes
1
answer
151
views
1
answers
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.taklifi • 60
Latest awards to pt.taklifi
Supporter
21 days ago,
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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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