User: gokberk

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gokberk20
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Posts by gokberk

<prev • 22 results • page 1 of 3 • next >
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HiSAT2 edit distance option
... Hi all, I'm analyzing single-end RNA-seq data and was wondering if there is a way to set the edit distance while using HiSAT2. It is not mentioned in the manual, should I somehow arrange the `--score-min` function? I was also wondering if there is an option like TopHat's `--microexon-search` to lo ...
rna-seq hisat2 written 1 day ago by gokberk20
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Unexpected characters at consensus fasta generated by mpileup
... Hi all, I'm using mpileup function on Linux (compiler: Ubuntu 4.8.4, samtools version 1.6-5-gfe1a2e9) to generate a consensus fasta using the following command: samtools mpileup -uf human_nanogv2.fa --bam-list bam_list | bcftools call -c | vcfutils.pl vcf2fq > consensus.fa This command cre ...
samtools consensussequence mpileup written 3 days ago by gokberk20
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Comment: C: featureCounts - annotation file issue
... Thanks for the advice geek_y! While I was trying to do what you suggested, I realized that the chromosome names in my gtf file and the chromosome names that are given at NCBI's website that I downloaded this gtf file do not match. So, I found the correct chromosome name from the gft file itself and ...
written 8 days ago by gokberk20
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featureCounts - annotation file issue
... Hi all, I've been using featureCounts to generate count tables out of my bam files. Previously, it worked fine with bam files which I generated with Subread. Now, I'm using featureCounts with the bam files I generated with HiSAT2. However, non of the alignments were assigned to any genes, since th ...
rna-seq written 8 days ago by gokberk20
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Comment: C: Subread alignment issue
... I guess I've more than 50 gb of memory on server, is it possible that it requires even more? ...
written 21 days ago by gokberk20
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Subread alignment issue
... Hi everyone, I'm trying to map two fastq files to M. fascicularis genome using the following command: ./subread-align -t 0 --sortReadsByCoordinates -T 5 -i ../../subread_index_normal/Macaca_fascicularis_5.0_genome -r ../../../../disk1/goekberk/SRR_files/SRR7529837_2.fastq -o BAM_files/SRR75298 ...
rna-seq written 21 days ago by gokberk20
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Comment: C: Generating count table
... Yes, I found it and solved my problem, thanks a lot! ...
written 21 days ago by gokberk20
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Generating count table
... Hi all, I've been trying to calculate TPM values for a count table, thus I've been using biomaRt package to obtain gene lengths. However, I'm using an NCBI annotation file and my count table has gene_name's as row names (I'm using gene_name instead of gene_id, because I receive an error otherwise). ...
rna-seq written 21 days ago by gokberk20
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Annotation problem while using Rsubread
... Hi all, I've been trying to read some bam files using Rsubread. As for the annotation file, I converted a gff file to gtf using `gffread`. Here is how my gtf file looks like: NC_012670.1 RefSeq exon 543 614 . + . transcript_id "rna76575"; NC_012670.1 RefSeq exon 615 1562 . + . transcript_i ...
gtf annotation gff written 24 days ago by gokberk20
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Comment: C: Browsing mappings for multiple BAM files
... It worked perfectly, thanks a lot! ...
written 6 weeks ago by gokberk20

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Supporter 6 days ago, voted at least 25 times.

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