User: chefarov

gravatar for chefarov
chefarov120
Reputation:
120
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Trusted
Location:
Greece
Twitter:
chefarov
Last seen:
1 month, 3 weeks ago
Joined:
5 years, 6 months ago
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c*******@gmail.com

Posts by chefarov

<prev • 32 results • page 1 of 4 • next >
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Comment: C: How To Filter Mapped Reads With Samtools
... `samtools view -bq 1 file.bam > unique.bam` This doesn't make sense at all. My best bet would be to compare XS with AS score. ...
written 7 weeks ago by chefarov120
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Comment: C: Question: Samtools Select SAM Flag for unpaired uniquely reads
... You may want to add `-F 4` to remove unmapped reads, and `-h` to keep the headers so that SAM/BAM viewers can read that file. The command I use (removes also reverse complements) is : samtools view -h -F 4 -F 16 -F 256 alignments.sam | grep -E "@|NM" | grep -v "XS:" > uniq_noRev.sam However ...
written 7 weeks ago by chefarov120
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Comment: C: Convert multiple-sequence fasta file to single long sequence
... This way it deletes the newlines as well cat multi.fasta | grep -v '^>' | grep '^.' | tr -d '[:blank:]' | tr -d '\n' | cat <( echo '>seq_name') - > multi_concat.fasta ...
written 10 weeks ago by chefarov120 • updated 28 days ago by RamRS25k
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Small DNA-seq read files for tests
... I am trying to find small dna-seq raw reads to experiment with some de-novo assembly techniques. I was looking for a list on ncbi but it seems you have to search for a specific SRA instead. Any ideas? ...
dna-seq next-gen written 13 months ago by chefarov120
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Comment: C: NCBI API for finding accession numbers?
... These are not APIs. It seems that there isn't anything that looks like API unfortunately. ...
written 14 months ago by chefarov120
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bowtie2 messes up headers with sequences in output
... I have a `query.fasta` file that looks like: >seq0 hello_world GAACCTAAGTACGCG ... >seq83 hello_world CACGCGGCTAGTACG ... >seq1170 hello_world CGTACTAGCCGCGTG ... >seq4420 hello_world CGCGTACTTAGGTTC ... Every sequence in this file is ** ...
bowtie2 sam written 24 months ago by chefarov120 • updated 24 months ago by michael.ante3.5k
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Comment: C: SAM/BAM: Extract sequences which aligned once and also don't overlap with any ot
... @Pierre Lindenbaum Thank you for your comments. I haven't still figured out what exactly a "tiling path of reads" is but this seems helpful. Apparently I would be interested in overlapping removal as well :) Could you provide some reference about the tiling path thing for me to check out? ...
written 24 months ago by chefarov120
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SAM/BAM: Extract sequences which aligned once and also don't overlap with any other sequence
... I used bowtie2 to do the alignments. Do you think that the methodology described below is correct? 1) To extract the reads that align only once grep -E "@|NM:" alignments.sam | grep -v "XS:" > unique.sam Now I am looking for a way to find which reads' alignments **don't overlap** with a ...
bowtie2 alignment samtools sam bam written 2.0 years ago by chefarov120
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Comment: C: How to extract unique mapped results from BWA results?
... This produces empty file in my case, whereas if I try this on the equivalent sam file: `grep -E "@|NM:" my.sam | grep -v "XS:" > my.sam.unique` seems to work. However my sam is produced by bowtie2 (if that's the cause of the confusion) ...
written 2.0 years ago by chefarov120
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Comment: C: Extract uniquely mapped reads from bam file
... I don't understand why mapping quality >= 5 means uniquely mapped :( ...
written 2.0 years ago by chefarov120

Latest awards to chefarov

Good Question 12 months ago, asked a question that was upvoted at least 5 times. For Is Paired End analysis possible with FASTQC?
Epic Question 12 months ago, created a question with more than 10,000 views. For Is Paired End analysis possible with FASTQC?
Popular Question 12 months ago, created a question with more than 1,000 views. For Clustering Blast overlapping alignments
Appreciated 12 months ago, created a post with more than 5 votes. For Is Paired End analysis possible with FASTQC?
Great Question 23 months ago, created a question with more than 5,000 views. For Is Paired End analysis possible with FASTQC?
Popular Question 23 months ago, created a question with more than 1,000 views. For Is there a DNA de-novo assembler parallelized for PBS/torque environment?
Popular Question 23 months ago, created a question with more than 1,000 views. For DNA de-novo assembly for plants different than rest organisms?
Student 23 months ago, asked a question with at least 3 up-votes. For Is Paired End analysis possible with FASTQC?
Supporter 2.1 years ago, voted at least 25 times.
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Is Paired End analysis possible with FASTQC?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For De-Novo Assembly pipeline on hadoop

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