User: bayramliaziz

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Posts by bayramliaziz

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Comment: C: How to get output with read counts and read count percentages from bam file?
... I aligned to the genome by using bwa aln after that I used samtools to get bam file. I am new to this thing so I am just trying to explore and experiment with different approaches. I'll check out the featurecounts. ...
written 11 months ago by bayramliaziz0
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How to get output with read counts and read count percentages from bam file?
... I have a bam file with lots of genes included and I would like get read counts and their percentages as a bam file. I tried samtools idxstats but It doesn't give percentages. Is there any tool that can do what I want? If there is I would like to get you opinion. Also my bam file is derived from pai ...
read counts picard samtools bam written 11 months ago by bayramliaziz0 • updated 11 months ago by WouterDeCoster43k
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Comment: C: How to trim primers with cutadapt from .fastq.gz file?
... When I use -a and -A, I get the following warning: WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above. But when I use -g and -G, It deletes whole gene again. When I look at the IGV, I see trimmed genes. ...
written 11 months ago by bayramliaziz0
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How to trim primers with cutadapt from .fastq.gz file?
... I tried to trim primers from my fastq.gz files with cutadapt, but It trims whole a lot than I intended. In same cases It trims whole genes. The command I used for trimming: cutadapt -a file:reverse.fasta -G file:forward.fasta -o out_R1.fastq.gz -p out_R2.fastq.gz in_R1.fastq.gz in_R2.fastq.gz ...
primer tool trim cutadapt written 11 months ago by bayramliaziz0 • updated 11 months ago by finswimmer13k
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Comment: C: How to align given specific region in genome with manifest file in bwa?
... samtools view -b -L manifest.bed -U non-overlapping.bam input.bam > overlapping.bam I used both options this way. But this time my overlapping.bam changed and It is not the same output with only -L. I am newbie so, I am sorry If I can not see the obvious. ...
written 11 months ago by bayramliaziz0
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Comment: C: How to align given specific region in genome with manifest file in bwa?
... I tried that but I couldn't get it to work. It just gives me the same bam file. I changed -L with -U. ...
written 11 months ago by bayramliaziz0
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Comment: C: How to align given specific region in genome with manifest file in bwa?
... Thanks you helped me a lot. The following script did the job: samtools view -b -L manifest.bed input.bam > manifest_output.bam I have one more question. Script above outputs alignments overlapping with the manifest.bed file. Is it possible to get output with non-overlapping alignments? ...
written 11 months ago by bayramliaziz0
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Comment: C: How to align given specific region in genome with manifest file in bwa?
... If I can not do this with bwa then which tool can I use to do the alignments for certain region? ...
written 11 months ago by bayramliaziz0
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Comment: C: How to align given specific region in genome with manifest file in bwa?
... Manifest.txt is the file that specifies a reference genome and targeted reference regions to be used in the alignment step. This definition is from MiSeq System Guide. Manifest.txt is given to MiSeq, but I want this process done on computer. Example for manifest file and I would like to know If I c ...
written 11 months ago by bayramliaziz0 • updated 11 months ago by Pierre Lindenbaum126k
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How to align given specific region in genome with manifest file in bwa?
... Usually when I use alignment with bwa, I follow this script: bwa aln reference.fa sample.fastq.gz > sample.sai But this time I have manifest.txt and I want to target specific regions with this and I want to speed the alignment process with specific output. If It is possible in BWA, I would ...
genome alignment bwa manifest written 11 months ago by bayramliaziz0

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