Moderator: cpad0112
cpad0112 ♦ 11k
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Posts by cpad0112
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Comment:
C: Bam header editing
... you can use picard replace sam header. https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.0.0/picard_sam_ReplaceSamHeader.php ...
written 1 day ago by
cpad0112 ♦ 11k
0
votes
1
answer
94
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1
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... $ awk 'FNR==NR {a[$0]++; next} {if ($2 in a) print $0}' file1.txt file2.txt ...
written 3 days ago by
cpad0112 ♦ 11k
0
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1
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... output:
$ join -1 1 -2 2 <(sort -k1 test1.txt) <(sort -k2 test.txt) -o 2.1,2.2
ST-E00243:601:HWJFHCCXY:8:1101:19512:10468 512
ST-E00243:601:HWJFHCCXY:8:1101:19431:10468 9606
input:
$ cat test1.txt
2485233
2485231
2059665
2029516
512
2022430
20224 ...
written 3 days ago by
cpad0112 ♦ 11k
1
vote
1
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... sed 's/.*\(rs\w\+\).*/\1/g' test.txt
Col1
rs10136766
rs104894363
rs10774624
rs111647200
rs117306900
rs117306950
rs117306954
rs117306975
rs117306989
rs532891158
rs794728599
rs121913344
rs12979860
rs397518008
rs397518039
rs6837175 ...
written 4 days ago by
cpad0112 ♦ 11k
0
votes
1
answer
92
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1
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... $grep -Po '(?<=^|-)rs\w*' test.txt
rs10136766
rs104894363
rs10774624
rs111647200
rs117306900
rs117306950
rs117306954
rs117306975
rs117306989
rs532891158
rs794728599
rs121913344
rs12979860
rs397518008
rs397518039
rs6837175
r ...
written 4 days ago by
cpad0112 ♦ 11k
0
votes
1
answer
156
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1
answers
Comment:
C: Having trouble using wildcard
... You can check the file existence with following code. Please change the path as per your convenience:
for i in {17..34}; do if [ -e ./MBM1${i}_R1_001.fastq ]; then echo "exists";fi;done
@ https://www.biostars.org/u/40545/ ...
written 5 days ago by
cpad0112 ♦ 11k
0
votes
1
answer
156
views
1
answers
Comment:
C: Having trouble using wildcard
... I think OP code still has a problem (assuming that it is updated):
`in1=./temp_expt/Sample_MBM1${i}/MBM1${i}_R1_001.fastq`.. this would look only for `MBM118_R1_001.fastq` under `sample_MBM118` folder, but not for `MBM18*_R1_001.fastq`.
Error should be some thing like this: `Can't find file ./t ...
written 5 days ago by
cpad0112 ♦ 11k
0
votes
1
answer
156
views
1
answers
Comment:
C: Having trouble using wildcard
... well, this is confusing. Your code is supposed to throw a different error.
copy/pasted the code from OP:
for i in {17..34}; do bash bbmap/bbsplit.sh in1=./temp_expt/Sample_MBM1${i}/MBM${i}_R1_001.fastq in2=./temp_expt/Sample_MBM1${i}/MBM1${i}_R2_001.fastq ref=./MG1655.fasta,./MGH78578.fasta,./ ...
written 5 days ago by
cpad0112 ♦ 11k
0
votes
0
answers
87
views
0
answers
... edgeR has a function for CPM calculation from counts ...
written 5 days ago by
cpad0112 ♦ 11k
3
votes
0
answers
147
views
0
answers
... This is ad for selling the company/website services. Please tag accordingly. https://www.biostars.org/u/16084/ ...
written 5 days ago by
cpad0112 ♦ 11k
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For C: Problem installing Rgraphviz in R
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For A: convert SNP calls to amino acid change
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