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Core NGS Intro class zoom - Shared screen with speaker view
Dennis Mishler
01:14:26
could you reshow that command line?
Dennis Mishler
01:14:31
for the last action
Nandini Aiyappan
01:29:55
Flag 2 =1?
Gabriel Johnson
01:42:03
samtools view -F 0x4 -f 0x2 -q 20 yeast_pe.sort.bam > yeast_pe.sort.filt.bam
Anna Battenhouse
01:44:41
Need to add -b to ensure output is BAM format
Anna Battenhouse
01:45:12
samtools view -F 0x4 -f 0x2 -q 20 -b yeast_pe.sort.bam > yeast_pe.sort.filt.bam
Gabriel Johnson
01:45:56
samtools view -F 0x4 -f 0x2 -q 20 yeast_pe.sort.bam | grep -P '[HWI]' | wc -l
Nandini Aiyappan
01:46:15
Or samtools view -c yeast.sort.filt.bam
Dennis Mishler
01:47:41
What's the way of then dividing that by 2? can you pipe the output into Awk or something?
Eduardo Castro
02:38:29
sorry about that, had to reconnect
Anna Battenhouse
02:42:34
idev -m 20 -A UT-2015-05-18 -N 1 -n 24 --reservation=intro_NGS
Albert MacKrell
02:56:29
SO the bam file doesn't just contain the info about genes that get aligned to but all of the genes?
Denise Furr
03:04:23
Yes, I was kicked out.
Anna Battenhouse
03:04:37
idev -m 60 -A UT-2015-05-18 -N 1 -n 24 --reservation=intro_NGS
Nandini Aiyappan
03:23:06
grep -v Dubious to filter out the dubious reads?
Gabriel Johnson
03:23:46
cat sc_genes.bed awk '{if($8 != Dubious): print}'
Nandini Aiyappan
03:26:29
It should be field 8
Dennis Mishler
03:38:16
Will we get a link for recordings?
Nandini Aiyappan
03:38:23
Thanks Anna!
Claudia Jou
03:38:29
thanks Anna,,
Dennis Mishler
03:38:29
oh, gotcha!
Eric Young
03:38:48
thank you everyone!!! :)
Chloe Atallah
03:39:01
Thank you!
Luciano Cantu
03:39:13
Thank you!
Dennis Mishler
03:39:17
Thank you, Anna! And Vy and Riddhiman
Kathryn Thompson
03:41:42
Thank you!
Albert MacKrell
03:43:50
Thanks Anna!