User: theodore

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theodore20
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New User
Location:
Germany
Last seen:
4 months, 1 week ago
Joined:
3 years, 3 months ago
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Posts by theodore

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Comment: C: oligoMatch from ucsc
... that's the worst omission, ever made! thank you and sorry for my stupidity! ...
written 4 months ago by theodore20
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oligoMatch from ucsc
... Hallo people, one quick question, how does oligoMatch from ucsc (kent lab tools) works? I am asking because for some reason it does not work for me. I am downloading the oligomatch from ucsc exe folder (the 64bit version), I download the hg19 genome in fasta (i have also tried the 2bit) **hg19.fa** ...
oligomatch ucsc written 4 months ago by theodore20 • updated 4 months ago by Emily_Ensembl12k
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Comment: C: BWA 0.7.12 and Unique reads, -r, -c options, XA: and SA: optional tags on SAM ou
... if I am not mistaken the following as noted above should do it try to map with: bwa mem -t 8 -M -k 19 -r 1 -c 1 and then from the sam file, before converting it to bam do: samtools view -h -q 1 -F 4 -F 256 $3/$NOEXT1".sam" | grep -v "XA:Z" | grep -v "SA:Z" > $3/$NOEXT1"_mem.sam" the -F 256 appl ...
written 13 months ago by theodore20
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Comment: C: Correlation For Chip-Seq Data In R -Input Data Format
... I got a question for correlation type analyses. Why using coverage, (are we referring to genome coverage?) to calculate the coefficiency/correlation of chip-seq experiments and not using coordinates+read counts as in macs bed output? If I have only the bed files can I use your proposed method? Is ...
written 24 months ago by theodore20
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Comment: C: Bwa-Mem: Discriminate Between Reads Mapping Uniquely And Those Mapping In Multip
... While digging in to the SAM file, the optional flags and the option during samtools view conversion I could also see some other flags that do not make sense even if I use for single end reads for samtools view the options: -F 4 -F 256 -q 1 I still get the SA:Z and XA:Z optional flags. They appear t ...
written 2.1 years ago by theodore20
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Comment: C: YA BWA Unique reads, -r, -c options, XA: option on SAM,
... what would you think a proper background would be? experiment? propose of the analysis?   regarding the "what am I missing" question, it refers mostly to the observation of the existence of the SA:Z and XA:Z, optional flags, although I have followed the recommendations described in nummerous posts ...
written 2.1 years ago by theodore20
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Comment: C: YA BWA Unique reads, -r, -c options, XA: option on SAM,
... I will probably also post this question over to seqansewers   ...
written 2.1 years ago by theodore20
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Comment: C: YA BWA Unique reads, -r, -c options, XA: option on SAM,
... no one??? anyone??? ...
written 2.1 years ago by theodore20
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BWA 0.7.12 and Unique reads, -r, -c options, XA: and SA: optional tags on SAM output,
... So, I am using the following version of BWA Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.7.12-r1039 I got through a lot threads read answers and so on... still I am confused. I am performing ChIP or 4C seq. I get single end reads. I would like to get uniquely mapped read ...
bwa 0.7.12 unique reads mapping sam written 2.1 years ago by theodore20 • updated 20 months ago by Carambakaracho10
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Answer: A: manipulating text in linux enviroment
... cut -f 9 | sed 's/[0-9]* //' | sort | uniq -c | sed 's/* //' | awk '{print $2,$3"\t"$1}' I got it thanks to your recommendations. The above command/pipeline worked miracles for me ...
written 3.3 years ago by theodore20

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