User: Samad

gravatar for Samad
Samad90
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90
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Location:
France
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1 day, 23 hours ago
Joined:
8 years, 10 months ago
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s********@gmail.com

Posts by Samad

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Method to Check Fastq Completeness after Fastq-dump
... 17 months ago and no answer to thais question, i have the same issue here when dumping big files (~30G) and don't want to restart downloading, how to resume browken download with fast-dump? best ...
written 17 months ago by Samad90
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Answer: A: wigCorrelate Error "Please remove overlaps and try again"
... I have the same error when converting wig to bigwig :Overlap on chr1 between items starting at 0 and 0 wig head: variableStep chrom=chr1 3003560 0 3003561 0 3003562 0 3003563 0 ...
written 22 months ago by Samad90
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Comment: C: Samtools View: Only Forward Or Reverse Strand
... The option "-h" is important to further use of bam files. Need to keep the SAM header which is mondatory : samtools view -F 20 **-h** ... : forward strand ...
written 3.5 years ago by Samad90
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Answer: A: ChIPseek online tool, errors?
... The reply of @vchris_ngs made me thinking & verifying in details from where they comes the additional peaks, so I realize that it's normal to have maybe more peaks in total compared to the initial number, the reason is that 1 peak in the 1st list can possibly overlap (partially) two peaks in the ...
written 4.2 years ago by Samad90
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Comment: C: ChIPseek online tool, errors?
... Hi vchris,  It's very useful your reply, acually I have used bedtools intersect and wanted to visualize results as Venn diagram so I can see the unique and overlapped peaks! Your question in the previous post made me thinking & verifying in details from where they comes the additional peaks, s ...
written 4.2 years ago by Samad90
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Comment: C: ChIPseek online tool, errors?
... Sorry 267+932 was for another example of comparison (also different than total of initial list, and different of the two others), I updated the my post according the example in image. The colors changes (can't control it for this online tool), but the list is the same The comparison is done by fra ...
written 4.2 years ago by Samad90
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ChIPseek online tool, errors?
... I have used online tool of analysis and annotation of ChIP-seq data "chipseek" (http://chipseek.cgu.edu.tw/ published here http://www.biomedcentral.com/1471-2164/15/539). When I compare two lists of peaks to get VennDiag (ovelapping peaks), I get different results for the same list! In the example ...
chip-seq chipseek peak ovelapping venn written 4.2 years ago by Samad90
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Answer: A: How To Sort Sam File
... Hi,  I had the same question about sorting the sam files, here is another solution, using unix command:  grep -v '^[[:space:]]*@' test.sam | sort -k3,3 -k4,4n  > test.sorted.sam (source methylKit R package) ...
written 4.6 years ago by Samad90
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Answer: A: item's end higher than chrom size, wigToBigWig
... That worked thank you a lot!! I didn't know that this option could skip the errors So it shows me the errors of chrom size but the conversion continues and the bw file is created Thanks again Cheers   ...
written 5.0 years ago by Samad90
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item's end higher than chrom size, wigToBigWig
... Hello everyone,  When converting from wig to bigwig (*bw) using wigToBigWig program on hg19 genome I got the following error: bedGraph error line 30430242 of H3K36.wig: chromosome chr9_gl000201_random has size 36148 but item ends at 36160 How can the items end (in my wig) exceed the correspondin ...
wig bigwig wigtobigwig chr9_gl000201_random written 5.0 years ago by Samad90

Latest awards to Samad

Popular Question 3.4 years ago, created a question with more than 1,000 views. For ChIPseek online tool, errors?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For item's end higher than chrom size, wigToBigWig
Student 3.9 years ago, asked a question with at least 3 up-votes. For Retrieve The Fasta Nucleic Sequences Of A List Of Ncbi Accession Number Of Proteins
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Retrieve The Fasta Nucleic Sequences Of A List Of Ncbi Accession Number Of Proteins
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: error with bedtools slop
Scholar 5.6 years ago, created an answer that has been accepted. For A: error with bedtools slop
Great Question 8.8 years ago, created a question with more than 5,000 views. For Retrieve The Fasta Nucleic Sequences Of A List Of Ncbi Accession Number Of Proteins
Epic Question 8.8 years ago, created a question with more than 10,000 views. For Retrieve The Fasta Nucleic Sequences Of A List Of Ncbi Accession Number Of Proteins
Popular Question 8.8 years ago, created a question with more than 1,000 views. For Retrieve The Fasta Nucleic Sequences Of A List Of Ncbi Accession Number Of Proteins

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