User: luzglongoria

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luzglongoria40
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Posts by luzglongoria

<prev • 93 results • page 1 of 10 • next >
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Comment: C: Feature Counts how to identify each sample
... Thank you for your answer. The thing is that I have an only BAM file. I run STAR and created an unique BAM file with all the samples inside. Like this I saved time :) So I don't have these BAM file you refer to. ...
written 19 hours ago by luzglongoria40
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Feature Counts how to identify each sample
... Hi there, I have run an alignment by using STAR by using the --readFilesManifest option since I have several samples and I wanted to run it at once: STAR --runThreadN 20 --genomeDir /path/to/the/folder/ --readFilesManifest /path/to/the/file/samples.txt Like this I have an unique .bam file wit ...
featurecounts rna rna-seq genomereference written 20 hours ago by luzglongoria40
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Comment: C: Problem with qualimap BAM file
... Yes, I see now. So, is there any way of solve it? to modify SAM file? Maybe by doing... samtools reheader -c 'grep -v ^@RG' Aligned_mosquito.out.bam > Aligned_mosquito.out_2.bam ...
written 5 weeks ago by luzglongoria40
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Comment: C: Problem with qualimap BAM file
... samtools view -H Aligned_mosquito.out.bam | grep '^@RG' @RG ID:bm @RG ID:bm @RG ID:bm @RG ID:dpi8 @RG ID:dpi8 @RG ID:dpi8 @RG ID:dpi12 @RG ID:dpi12 @RG ID:dpi12 @RG ID:dpi22 @RG ID:dpi22 @RG ID:dpi22 @RG ID:control @RG ID:control @RG I ...
written 5 weeks ago by luzglongoria40
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Comment: C: Problem with qualimap BAM file
... Sure samtools view -h Aligned_mosquito.out.bam | head @HD VN:1.4 @SQ SN:NW_001889870.1 LN:1197 @SQ SN:NW_001889869.1 LN:1433 @SQ SN:NW_001889868.1 LN:1481 @SQ SN:NW_001889867.1 LN:1513 @SQ SN:NW_001889866.1 LN:1679 @SQ SN:NW_001889865.1 LN:1696 @SQ SN:NW_00188986 ...
written 5 weeks ago by luzglongoria40
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Comment: C: Problem with qualimap BAM file
... Thank you for your comment. I use `--readFilesManifest` instead of the one you suggest because in the manual indicate `--readFilesManifest` for mapping multiple reads files, especially convenient for a very large number of files. I created a manifest fi le containing 3 tab-separated columns. Please ...
written 5 weeks ago by luzglongoria40
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Problem with qualimap BAM file
... HI there, I have run STAR with the my reference genome. I got the SAM file that I converted in BAM file. Now, I want to see the quality of that file by using qualimap but I get this error: qualimap bamqc -bam Aligned_mosquito.out.bam -gff /genome_reference/mosquito/GCF_000209185.1_CulPip1.0_ge ...
qualimap bam bamfile error rna-seq written 5 weeks ago by luzglongoria40 • updated 5 weeks ago by Pierre Lindenbaum133k
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Comment: C: Problem when running FeatureCounts
... OMG!!!! I feel so stupid!!! thank you so much! It solved the problem ...
written 5 weeks ago by luzglongoria40
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Problem when running FeatureCounts
... Hi! I have run STAR for mapping my reads with my reference genome. I got a BAM file and now I want to run FeatureCounts in my server. However, despite I have read the manual it seems to be a problem with the input argument: featureCounts -a /path/to/genome_reference/GCF_000209185.1_CulPip1.0_ge ...
featurecounts rna bamfile error rna-seq written 5 weeks ago by luzglongoria40
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Comment: C: Error in STAR when mapping
... Thank you! However, my files are in .fq format. They are not compress. How can I do? ...
written 5 weeks ago by luzglongoria40

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