User: Heinrich_M

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Heinrich_M0
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Posts by Heinrich_M

<prev • 11 results • page 1 of 2 • next >
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Tool/Pipeline to get annotations from RNA-Seq
... Hello everyone, I need an automated way to generate and filter annotations of RNA-Seq data. I have a lot of RNA-Seq data to analyze and can't go through BLAST searches individually. I am looking for transposons (reverse transcriptase, ect. ) in repetitive elements in different stages of a parasite. ...
rna-seq blast written 9 months ago by Heinrich_M0
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Comparison of transcripts of different parasite stages - graphic output
... I have RNA-Seq data from different stages of a parasite and I am investigating only certain genome areas. I have already done a Deseq analysis and some of the genes are differentially expressed. Now I have merged the mapped reads to get the elongated reads, to get the whole RNA fragments. These RNAs ...
alignment rna-seq written 9 months ago by Heinrich_M0
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Comment: C: bcftools consensus failure
... Is there something wrong with the vcf file? ...
written 9 months ago by Heinrich_M0
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Comment: C: bcftools consensus failure
... Okay thanks, than `-s` is not necessary. The sample has the following header: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT mapped_male_replicate.bam W003_0-161190 154995 . G A7.30814 . DP=2;VDB=0.18;SGB=-0.453602;MQ0F=0;AC=2;AN=2;DP4=0,0,2, ...
written 10 months ago by Heinrich_M0
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getting consensus sequence with bcftools failed
... I want to extract the mapped regions out of bam files. So I tried bcftools. I have the current version of bcftools (V.19). I tried the following steps bcftools mpileup -Ou -f reference.fa alignments.bam | bcftools call -mv -Oz -o calls.vcf.gz after that a note appeared > Note: none of -- ...
genome vcf samtools rna-seq bcftools written 10 months ago by Heinrich_M0
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Kegg result interpretation
... Hello, The kegg kaas analysis (https://www.genome.jp/tools/kaas/) shows many pathways as a result. For a publication I wanted to test the significance of the pathways. Is a fisher exact test the right choice? Is it even necessary to test the significance of the pathways? Unfortunately I could not fi ...
gene R statistic rna-seq written 13 months ago by Heinrich_M0
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Comment: C: Process RNA-Seq Data with specific sequences / not whole reference genome
... Yes I have the GFF File, but I guess it just contains the genes and I'm searching for repetitive elements. And I have still the error with the gene_id when matching the Genoic GFF against the BAM file. Is there an option to count the sequences without greating a GFF file? ...
written 14 months ago by Heinrich_M0
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Comment: C: Process RNA-Seq Data with specific sequences / not whole reference genome
... Okay, my fault. I guess the BAM file is good. But the gff is not. Now these files are not comparable. Is there an option to count the sequences without greating a gff file? ...
written 14 months ago by Heinrich_M0
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Comment: C: Process RNA-Seq Data with specific sequences / not whole reference genome
... Then I have to create a GFF file from the sequences (I already did that, but then an error message is displayed Fatal error: Unknown error occured [bam_sort_core] merging from 1 files and 1 in-memory blocks... Error occured when processing GFF file (line 3 of file /home/galaxy/galaxy/database/files/ ...
written 14 months ago by Heinrich_M0
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Comment: C: Process RNA-Seq Data with specific sequences / not whole reference genome
... I did a blast alignment and then converted it to a bed file by adding values. With Bed-to-GFF I had the GFF for htseq. As Bed file I had the reads mapped against the reference genome. but, as you can see, i don't know how to use it well yet and maybe that's not a good approach. ...
written 14 months ago by Heinrich_M0

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