User: yelekley7

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yelekley70
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Posts by yelekley7

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Comment: C: how to capture vcf's INFO field with bcftools
... Thanks, sorry for a simple question but how do I redirect the output to a text file of my choice? Sorry, i got it. my $cmd2 = `bcftools query $vcf_indexed -f '%CHROM\t%POS\t%REF\t%ALT\t%INFO/ANN][\t%SAMPLE=%AD]\n' --samples '$sample' > $output_file`;print $cmd2; ...
written 9 days ago by yelekley70
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how to capture vcf's INFO field with bcftools
... Hello, I'm trying to print the content of a vcf file but having problem with capturing the 'INFO' column. Here is the code. my $cmd2 = `bcftools query $vcf_indexed -f '%CHROM\t%POS\t%REF\t%ALT\t%INFO/TAG[\t%SAMPLE=%AD]\n' --samples '$sample'`;print $cmd2; I get "Error: no such tag defined i ...
software error written 9 days ago by yelekley70 • updated 9 days ago by Pierre Lindenbaum101k
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Comment: C: How to achieve the same alignment with HiSAT2 command line vs. HiSAT2 Galaxy
... I ran: samtools flagstat glaxy.bam and it looks like the stats are comparable: 345063 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 586 + 0 mapped (0.17%:-nan%) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 ...
written 24 days ago by yelekley70 • updated 24 days ago by genomax37k
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Comment: C: How to achieve the same alignment with HiSAT2 command line vs. HiSAT2 Galaxy
... @Devon. When I click on "i" Dataset information, Job information and Tool parameters are displayed. I don't see any commands. Here what is says for Tool version. Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.5.2 Galaxy Tool Version: 2.0.5.2 Tool Version: /galaxy/m ...
written 24 days ago by yelekley70 • updated 24 days ago by genomax37k
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How to achieve the same alignment with HiSAT2 command line vs. HiSAT2 Galaxy
... Hello, I've created a small reference fasta file that consists of combined sequences of two exons from two different genes where I know the fusion has occurred. I've uploaded that reference file into Galaxy as well as a fastq file and ran the tool with all default setting. The alignment worked per ...
rna-seq written 24 days ago by yelekley70 • updated 24 days ago by Devon Ryan73k
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Comment: C: hisat2 command line fastq to bam
... Yes, thank you for your help. I did not include any [options*] since I'm indexing the entire hg19 file. I hope that was correct. ...
written 24 days ago by yelekley70
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Comment: C: hisat2 command line fastq to bam
... I indexed hg19 with Samtools and but with HISAT2, therefore, i need to index it, correct? I find the Manual very confusing. From what I can understand the following command input should produce and index for hg19 file, with hg19_indexed as the output that can be used in next alignment step, correct ...
written 24 days ago by yelekley70
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hisat2 command line fastq to bam
... Hello, Could someone please suggest Linux command line for RNA HISAT2 alignment of single fastq with to ucsc hg19 fasta already saved and indexed? I would like to generate a bam file. I've tried it on Galaxy and now would like to reproduce on the command line, but the syntax is not clear. Do I n ...
rna-seq written 25 days ago by yelekley70
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Indel detectors for Ion Torrent data
... Hello, Could someone please suggest a good indel detector to use on IonTorrent BWA-Mem aligned bam files. I've tried Pindel and achieved good results, however, some indels are still missed. Thanks ...
indel written 4 weeks ago by yelekley70 • updated 4 weeks ago by Kevin Blighe7.3k
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Comment: C: how to make a .bam file from fastQ for RNA-seq ion torrent with BBmap
... I got it to make sam file but samtools crashes when I tried to sort that file. ...
written 5 weeks ago by yelekley70

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Popular Question 3 months ago, created a question with more than 1,000 views. For convert fasta dna files to protein

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