How do I download BAM file from (GIGA)DB?
1
Hello Everyone,
I am trying to download some BAM files from GIGA(DB).
http://gigadb.org/dataset/view/id/100355/File_page/14
However, I am not being able to download it. Whenever I try, it shows network error after some moments. I would like to know if there is some solution to this. Thank you.
BAM
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updated 13 months ago by
Ram
43k
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written 20 months ago by
tf
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0
it works on my side. Talk to your sysadmin (proxy settings...)
$ wget -q -O - "https://ftp.cngb.org/pub/gigadb/pub/10.5524/100001_101000/100355/transcript-alignments/LowAltitude_cattle_lung_2.bam" | samtools view | head
HWI-ST1307:161:C3UG9ACXX:4:2112:15873:27236 163 1 1044 50 100M = 1097 153 CTCCAACAACATAGGAACATAGCCCTGAACATTAAAATACAGGCTGCCCAACGTCATGTCAAACCCATAGATGCCCCAAAACTCACTCCTGGACACTTCA CCCFFFFFHHHHHJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJGHIHIJIJJJIIIJJJHHHHHFFFFFDDDEDDDDDDDDDDDDDDDDDDDD AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YT:Z:UU NH:i:1 XS:A:+
HWI-ST1307:161:C3UG9ACXX:4:2112:15873:27236 83 1 1097 50 100M = 1044 -153 TCATGTCAAACCCATAGATGCCCCAAAACTCACTCCTGGACACTTCATTGCACTCCAGAGAGAAGAGATCCAGTTCCACTGACCAGAACACAGATGCAAG CDDCCA???>DDEDEEEEFFFHFHDGG@FCF=HEJIJIIGF?JIIJJIHIHIJGJIIJJJJIIJIIJJJJIJJIGJIHJJJIJJJJIHHHHHFFFFFCCC AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:79C20 YT:Z:UU NH:i:1 XS:A:+
HWI-ST1307:161:C3UG9ACXX:4:2212:15874:29325 163 1 1685 3 100M = 1781 196 GGAAAAAGAAGAAAGAATTAAAACAAATGAGGACAACCTCAGAGGCCTCTGCGACAATGTTAAATGCCCCAACATTTGAATCATAGGAGTCTCAGCAGAA BC@FFFFFFHHHHJJIIIIJJJJJJIGGIJJJJJIJJJJJIIJIIJJIIIHIIIIJIGGHHHHGDHDEFFDDDDDDFEDDDDDDDDDDDCDDDEDDDDDD AS:i:-11 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:6C12G80 YT:Z:UU NH:i:2 CC:Z:7 CP:i:42372672 XS:A:+ HI:i:0
HWI-ST1307:161:C3UG9ACXX:4:2212:15874:29325 83 1 1781 3 100M = 1685 -196 AGAAGACAACAAAAAGAAAGGGCATGAGAAAATACCTGAGGAGATAATAGTTGAAATTTTCTCTAAAATGGGGAAGGAAATAGCCACCAAAGCCCAAGAA DDDDDDDDEDEEFFFFFFHHHHHJIJJIIJIGHFJIIIIJJJJJJJJGIIJJJIJIIJJJJJIJJJJIIJJJJJJJJJJIHJJHFEJGGHHGFFFFFCCC AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7G92 YT:Z:UU NH:i:2 CC:Z:7 CP:i:42372576 XS:A:+ HI:i:0
HWI-ST1307:161:C3UG9ACXX:4:2301:3428:46249 163 1 3328 50 100M = 3378 150 GAAAAAGAAACAAAGGAGGCTATAGCAAAAATCAACAAAACTAACAGCTGGTTCTTTGAGAAGATAAATAAAATAGACAAACCATTAGCCAGACTCATCA CCCFFFFFHHHHHJJIJJJJJJIJJJIJJJJJIIIJJIJJJJJIJJJJIJHIIJJJJJIJJJJIIJHHHHHHFFFFFFDEEDDDDCDDDDDDDDDDDCDD AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:9G90 YT:Z:UU NH:i:1 XS:A:+
HWI-ST1307:161:C3UG9ACXX:4:1108:18449:7446 163 1 3331 50 100M = 3424 193 AAAGAAACAAAGGAGGCTATAGCAAAAATCAACAAAACTAACAGCTGGTTCTTTGAGAAGATAAATAAAATAGACAAACCATTAGCCAGACTCATCAAGA CCCFFFFFHHHHGIJJIGIGGHIIJIJJJJIJJJGIJJJJJJJGGIJJGIFGIJJIIIIJGJJJJJJJJHHHHHHFFEFDDEEEEDDDDBDDDDDDDCDC AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G93 YT:Z:UU NH:i:1 XS:A:+
HWI-ST1307:161:C3UG9ACXX:4:2301:3428:46249 83 1 3378 50 100M = 3328 -150 GTTCTTTGAGAAGATAAATAAAATAGACAAACCATTAGCCAGACTCATCAAGAAAAAAAGGAGAAAATCAAATCAACAAAATTAGAAATGAAAATGGAGA DDDDDCA@CCFC@D@FFD@FFFEECFHFIHEJGHCGJJIIHGHGIIHEJJJJJJIJJJJIJJJJJIHCJJJIHJJHJJJJIHGJJIJHFHHHFFFFFCCC AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YT:Z:UU NH:i:1 XS:A:+
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