User: luzglongoria
luzglongoria • 40
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Posts by luzglongoria
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... 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
luzglongoria • 40
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... 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 ...
written 20 hours ago by
luzglongoria • 40
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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
luzglongoria • 40
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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
luzglongoria • 40
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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
luzglongoria • 40
0
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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
luzglongoria • 40
1
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1
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... 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 ...
written 5 weeks ago by
luzglongoria • 40
• updated
5 weeks ago by
Pierre Lindenbaum ♦ 133k
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... OMG!!!!
I feel so stupid!!! thank you so much! It solved the problem ...
written 5 weeks ago by
luzglongoria • 40
5
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1
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128
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... 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 ...
written 5 weeks ago by
luzglongoria • 40
0
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174
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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
luzglongoria • 40
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