User: camelest

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camelest10
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Posts by camelest

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Comment: C: Segmentation fault (core dumped) error with bigWigAverageOverBed
... Thank you for your input. I also encountered some posts stating that. But if its memory problem, shouldn't splitting the file solve the problem? ...
written 7 weeks ago by camelest10
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Comment: C: Segmentation fault (core dumped) error with bigWigAverageOverBed
... Thank you for your comment. I think something like "1,Chr1" is output of the code Pierre Lindenbaum suggested. 1 is the result of int($3)-int($2) in printf, if I understand correctly (sorry I'm pretty new to this area). The below code gives me the usual Chr orders. awk '{print $1}' INPUT.bed ...
written 7 weeks ago by camelest10
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Comment: C: Segmentation fault (core dumped) error with bigWigAverageOverBed
... Thank you for your help. So it seems that there is something wrong in Chr column with my BED file. I used bigWigtobedGraph and the result is something like this. bigWigToBedGraph input.bw output.bedGraph chr1 629903 629904 1 chr1 629909 629910 1 chr1 629916 629917 1 ...
written 7 weeks ago by camelest10
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Comment: C: Segmentation fault (core dumped) error with bigWigAverageOverBed
... Thank you for your input. These are the results. file INPUT.bed input.bw INPUT.bed: ASCII text input.bw: data awk '{printf("%d,%s\n",int($3)-int($2),$0);}' INPUT.bed | sort -t, -k1,1n | head 1,chr1 100000358 100000359 chr1:100000358-100000359,+ 0 + 1,chr1 10002693 10002694 ...
written 7 weeks ago by camelest10
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Segmentation fault (core dumped) error with bigWigAverageOverBed
... I'm wondering someone could help about the error on bigWigAverageOverBed. My system is Ubuntu 18.04.4 LTS and bigWigAverageOverbed is v357. I'm encountering an error with a simple code as below, bigWigAverageOverBed input.bw INPUT.bed output.tab which gives me back as processing chromoso ...
bigwigaverageoverbed rna-seq written 7 weeks ago by camelest10 • updated 7 days ago by Biostar ♦♦ 20
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Comment: C: How to extracts reads with exact match with BBDuk?
... Thank you for your comment. This was really helpful. ...
written 5 months ago by camelest10
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Comment: C: How to extracts reads with exact match with BBDuk?
... Sorry for the late reply. Thank you so much for your input. I found that you are totally correct. Is there any good ways in order to extract paired-ends with only read2 starting with TTTTT but not read1? I was thinking only use the read2 file as the input, do the same thing and use `repair.sh in1=re ...
written 5 months ago by camelest10
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How to extract reads with exact match with BBDuk?
... Hi, I'm pretty new to this area and is wondering anyone could help. I have a pair-ended RNA-seq data. What I'd like to do is to extract reads with a certain sequence in the 5' end of read2 from a fastq file, for example TTTTT. I've tried with BBDuk as below. bbduk.sh -Xmx1g in1=read1.fastq in2= ...
fastq bbduk rna-seq written 5 months ago by camelest10

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