User: beginner

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beginner20
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Posts by beginner

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Comment: C: Error in extracting Counts from the bam file using htseq-count
... Basically I haven't used any gtf file in the alignment step. I'm using a standard genome index from hisat2 website. And now I stripped the "chr" from the gtf file. I will use this gtf file for stringtie and other steps. Is this ok? Or should I build own genome index? ...
written 1 day ago by beginner20
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Comment: C: Error in extracting Counts from the bam file using htseq-count
... You are right. They look different in the sorted.abm file it is without "chr" and in gtf file I see "chr". I gave it like this `cat gencode.v27.primary_assembly.annotation.gtf | sed 's/chr//' > gencode.v27.primary_assembly.annotation_nochr.gtf` Using htseq-count now. ...
written 1 day ago by beginner20
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Comment: C: Error in extracting Counts from the bam file using htseq-count
... I actually Gave this way and it worked but I don't see any counts. `htseq-count –s reverse -q –f bam sample1.sorted.bam gencode.v27.primary_assembly.annotation.gtf > sample1_counts.txt` ENSG00000000003.14 0 ENSG00000000005.5 0 ENSG00000000419.12 0 ENSG00000000457 ...
written 1 day ago by beginner20
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Comment: C: Error in extracting Counts from the bam file using htseq-count
... I didn't mention the paths here. The command for htseq-count I gave above is the right one. I didn't install the program. ...
written 1 day ago by beginner20
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Error in extracting Counts from the bam file using htseq-count
... Hi, I'm trying to extract counts for each gene from the sorted.bam file using htseq-count. But I end with an error. Command I used: htseq-count –s reverse –f bam –q sample.sorted.bam gencode.v27.primary_assembly.annotation.gtf > sample1_counts.txt I have this error: /path/soft/apps/HT ...
htseq bam counts rna-seq written 1 day ago by beginner20 • updated 1 day ago by h.mon11k
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Comment: C: Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
... I tried with this: htseq-count –s reverse –f bam –q sample1.sorted.bam gencode.v27.primary_assembly.annotation.gtf > sample1_counts.txt I have this error: /path/soft/apps/HTSeq/0.6.1p1-goolf-1.7.20-Python-2.7.11/bin/htseq-count: Error: Please provide two arguments. Call with '-h' to get usa ...
written 2 days ago by beginner20
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Comment: C: Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
... Could you please tell something about my previous comment. ...
written 2 days ago by beginner20
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Comment: C: Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
... I would like to use htseq-counts. htseq-count -f bam -q sample1.bam gencode.v27.primary_assembly.annotation.gtf > sample1_counts.txt Is this right for strand-specific (RF)? Is bam fine or I need to give sorted.bam? And could you please tell how to strip "chr" from gtf file in linux. ...
written 3 days ago by beginner20
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Comment: C: Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
... Hello Devon, Sorry for asking you again. The "MSTRG" in the above stringtie_merged.gtf file are the novel transcripts? because I see some with Ensembl gene id and transcript id. I think that if stringtie doesn't find any ref gene locations from gtf file but finds rna-seq alignments in that location ...
written 3 days ago by beginner20
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Comment: C: Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
... It was already mentioned in the above question. I gave a A133_GRCh38.gtf file output. ...
written 12 days ago by beginner20

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