User: amitpande74
amitpande74 • 10
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Posts by amitpande74
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2
votes
3
answers
76
views
3
answers
... HI,
I have paired end reads, and want to extract reads which have the insert `TGTATGTAAACTTCCGACTTCAACTGTA`in them.
I tried with `grep -A2 -B1 "TGTATGTAAACTTCCGACTTCAACTGTA" input.fq |grep -v "^\-\-$"` > 1.fq and 2.fq
But they dont align with Bowtie2 anymore, because the reads have differing head ...
written 11 days ago by
amitpande74 • 10
• updated
11 days ago by
GenoMax ♦ 95k
0
votes
0
answers
96
views
0
answers
Comment:
C: complexheatMap runtime error
... Shall check if this is the case. ...
written 28 days ago by
amitpande74 • 10
1
vote
0
answers
96
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0
answers
... HI,
I tried running heatmap from complexheatmap package. It gives an error:
Listening on http://127.0.0.1:5089
Warning: Error in : Heatmap name cannot be empty string.
215: stop
214: stop_wrap
213: Heatmap
212: eventReactiveHandler [/home/amit/Downloads/Shiny-master/ ...
written 28 days ago by
amitpande74 • 10
1
vote
1
answer
176
views
1
answers
Comment:
C: bowtie2 shell script
... (base) usr@usr-X705UDR:/media/usr/Elements/usr$ ./bowtie.sh
+ MYPATH=/media/usr/Elements/usr/Extracted_SB_reads
+ find /media/usr/Elements/usr/Extracted_SB_reads -maxdepth 3 -type -f name '*.fq$'
find: Unknown argument to -type: -
Stops here.
So corrected it to:
#!/bin/bash - ...
written 5 weeks ago by
amitpande74 • 10
0
votes
1
answer
176
views
1
answers
Comment:
C: bowtie2 shell script
... Hi,
Thanks for your help. These fastq files are not very big, as only those reads which have the transposon and the guide RNA have been extracted (wgs).
I tried running it script though, and it gave an error:
(base) usr@usr-X705UDR:/media/usr/Elements/usr$ ./bowtie.sh
+ MYPATH=/media/usr/ ...
written 5 weeks ago by
amitpande74 • 10
0
votes
1
answer
176
views
1
answers
Comment:
C: bowtie2 shell script
... These are reads extracted for a transposon and guideRNA. They have to be aligned to the human genome to determine the genomic location of their insertion.
(base) amit@amit-X705UDR:/media/amit/Elements/usr/Extracted_SB_reads$ ls
B2DNA_extractedSB DNA27.extractedSB DNA4.extractedSB H1DNA ...
written 5 weeks ago by
amitpande74 • 10
0
votes
1
answer
176
views
1
answers
Comment:
C: bowtie2 shell script
... I did.
for i in /media/usr/Elements/usr/Extracted_SB_reads/C1DNA.extrSB/*.fq
do
bowtie2 --sensitive-local -p8 -x /media/usr/Elements/usr/bowtie2_index/hg19/ -U ${i}.fq -S $i.sam
done
and now it says:
(ERR): bowtie2-align exited with value 1
stat: Bad file descr ...
written 5 weeks ago by
amitpande74 • 10
6
votes
1
answer
176
views
1
answer
... Dear All,
I have tons of folders inside which I have fastq files, and these are single end reads.![folders][1] ![files][2]
I want to write a shell/bash script to automate the alignment.
for i in /media/usr/Elements/name/Extracted_SB_reads/C1DNA.extrSB/*.fq
do
bowtie2 --sensitive ...
written 5 weeks ago by
amitpande74 • 10
• updated
5 weeks ago by
ATpoint ♦ 44k
0
votes
0
answers
139
views
0
answers
Comment:
C: bowtie2 making new indices
... Primarily the genomic locations where the transposon has inserted ...
written 6 weeks ago by
amitpande74 • 10
0
votes
0
answers
139
views
0
answers
Comment:
C: bowtie2 making new indices
... The transposon and the gDNA are seen in the SAM file, but downstream processing of the SAM file into BAM and BAM to BED does not result into the chromosome numbers. It looks like this
chr 123 456
So while the reads are being retrieved in the SAM files, I cannot trace the genomic coordinates. ...
written 6 weeks ago by
amitpande74 • 10
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