User: Sam

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Sam70
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9 months, 3 weeks ago
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Posts by Sam

<prev • 117 results • page 1 of 12 • next >
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compare two columns in text files
... Dear Biostars I have two files and I want compare file 1 with column 4 of file 2 and print matched line file2 to file3. but I want keep the header line of file2 , so is it a correct code : Thanks ---------- cat <(head -n 1 file2) <(awk -F '\t' 'NR==FNR{a[$1]++;next} (a[$4])' fil ...
cat awk written 13 days ago by Sam70
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add header with awk
... Dear All I filtered a tab file with this command awk -F'\t' '$15~/NO/' famliy.txt but I want add header of input file to the out file with filtering command (one line command). Thanks ...
awk written 13 days ago by Sam70 • updated 13 days ago by toralmanvar420
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Comment: C: text file editing
... alleles are G/T-A/C but for this command "awk -v OFS="\t" '{print $1,$2,$3,$4,$5,$6"/"$7,$8,$11,$12}' test.txt | datamash -g1 unique 2 unique 3 collapse 4-9 | awk -v OFS="\t" '{gsub(",","-");gsub("-",",",$2)}1' " I got error : datamash: -H or --header-in must be used with named columns ...
written 23 days ago by Sam70
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text file editing
... Dear ALL I have about 200 tab delimited and in first step I want merge them to have a comprehensive file, then want to summarize file to have another out put, so in summarize file just keep unique ID in 1st ,2nd and 3rd columns and for pos1 and pos2 add the number of number of lines with repetiti ...
awk bash written 24 days ago by Sam70 • updated 24 days ago by Pierre Lindenbaum110k
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Comment: C: appropriate script for DNA alignment
... maybe useful to others! I obtained better results with BWA MEM algorithm with default flags, I think the issue was the algorithm of alignment. I enjoyed your company ...
written 26 days ago by Sam70
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Comment: C: appropriate script for DNA alignment
... in GBS analysis in some pipeline is possible to merge the GBS data of some samples to prepare a reference for SNP variant analysis. so I have a GBS created ref and I want to align it to a reference genome of Populus. I think here the issue is the long sequence in mock ref file because I lost about 3 ...
written 26 days ago by Sam70
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Comment: C: appropriate script for DNA alignment
... it's a mock reference (which is created by merging of some GBS data of a tree sample) due to that is in fasta format. ...
written 26 days ago by Sam70
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Comment: C: appropriate script for DNA alignment
... already I tried bowtie2 with `-X 400 -I 100 --very-sensitive` but about 35 % of sequence could not match and I think the issue is the length of the sequence and seed region in alignment, what do you think? ...
written 26 days ago by Sam70 • updated 26 days ago by h.mon16k
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6 follow
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appropriate script for DNA alignment
... Dear Biostars I have a fasta file with about 100 K DNA sequences with length about 300bp , and I want to align them to a target genome to have bam output file, could you introduce me an appropriate script for this alignment? Thanks ...
alignment dna written 26 days ago by Sam70
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prepare a GFF file for MOCK fasta reference
... Dear Biostars I need your help to handle this problem, I'm working with GBS data and now I have a big list of SNP position in my output file and I used a mock reference for SNP variant analysis (merged some of GBS samples to prepare a mock ref). In the output file, I have the position of SNP accord ...
genome gff sequence written 27 days ago by Sam70

Latest awards to Sam

Supporter 9 weeks ago, voted at least 25 times.
Centurion 3 months ago, created 100 posts.
Rising Star 8 months ago, created 50 posts within first three months of joining.

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